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- PDB-6c5l: Conformation of methylated GGQ in the Peptidyl Transferase Center... -

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Basic information

Entry
Database: PDB / ID: 6c5l
TitleConformation of methylated GGQ in the Peptidyl Transferase Center during translation termination (T. thermophilus)
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 32
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
  • Peptide chain release factor 2
  • mRNAMessenger RNA
KeywordsRIBOSOME / methylated RF2 / translation termination
Function / homology
Function and homology information


translation release factor activity, codon specific / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...translation release factor activity, codon specific / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / Ribosomal protein L1, bacterial-type / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Peptide chain release factor 2 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Peptide chain release factor 2 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZeng, F. / Jin, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM120552 United States
CitationJournal: Sci Rep / Year: 2018
Title: Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.
Authors: Fuxing Zeng / Hong Jin /
Abstract: The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The ...The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S rRNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AV: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
AW: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
AX: mRNA
AY: Peptide chain release factor 2
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 50S ribosomal protein L30
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
B9: 50S ribosomal protein L36
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L1
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BJ: 50S ribosomal protein L10
BK: 50S ribosomal protein L11
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
CA: 16S rRNA
CB: 30S ribosomal protein S2
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14 type Z
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein Thx
CV: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
CW: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
CX: mRNA
CY: Peptide chain release factor 2
D0: 50S ribosomal protein L27
D1: 50S ribosomal protein L28
D2: 50S ribosomal protein L29
D3: 50S ribosomal protein L30
D4: 50S ribosomal protein L31
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
D9: 50S ribosomal protein L36
DA: 23S rRNA
DB: 5S rRNA
DC: 50S ribosomal protein L1
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: 50S ribosomal protein L10
DK: 50S ribosomal protein L11
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,648,016598
Polymers4,636,103118
Non-polymers11,913480
Water34219
1
AA: 16S rRNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AV: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
AW: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
AX: mRNA
AY: Peptide chain release factor 2
B0: 50S ribosomal protein L27
B1: 50S ribosomal protein L28
B2: 50S ribosomal protein L29
B3: 50S ribosomal protein L30
B4: 50S ribosomal protein L31
B5: 50S ribosomal protein L32
B6: 50S ribosomal protein L33
B7: 50S ribosomal protein L34
B8: 50S ribosomal protein L35
B9: 50S ribosomal protein L36
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L1
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BJ: 50S ribosomal protein L10
BK: 50S ribosomal protein L11
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,323,546280
Polymers2,318,05259
Non-polymers5,495221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S rRNA
CB: 30S ribosomal protein S2
CC: 30S ribosomal protein S3
CD: 30S ribosomal protein S4
CE: 30S ribosomal protein S5
CF: 30S ribosomal protein S6
CG: 30S ribosomal protein S7
CH: 30S ribosomal protein S8
CI: 30S ribosomal protein S9
CJ: 30S ribosomal protein S10
CK: 30S ribosomal protein S11
CL: 30S ribosomal protein S12
CM: 30S ribosomal protein S13
CN: 30S ribosomal protein S14 type Z
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein Thx
CV: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
CW: E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)
CX: mRNA
CY: Peptide chain release factor 2
D0: 50S ribosomal protein L27
D1: 50S ribosomal protein L28
D2: 50S ribosomal protein L29
D3: 50S ribosomal protein L30
D4: 50S ribosomal protein L31
D5: 50S ribosomal protein L32
D6: 50S ribosomal protein L33
D7: 50S ribosomal protein L34
D8: 50S ribosomal protein L35
D9: 50S ribosomal protein L36
DA: 23S rRNA
DB: 5S rRNA
DC: 50S ribosomal protein L1
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: 50S ribosomal protein L10
DK: 50S ribosomal protein L11
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,324,470318
Polymers2,318,05259
Non-polymers6,418259
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.023, 452.527, 623.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B8
21chain D8
12chain AF
22chain CF
13chain AH
23chain CH
14chain BO
24chain DO
15chain BI
25chain DI
16chain B4
26chain D4
17chain BW
27chain DW
18chain AU
28chain CU
19chain BQ
29chain DQ
110chain AB
210chain CB
111chain AD
211chain CD
112chain BS
212chain DS
113chain AY
213chain CY
114chain AP
214chain CP
115chain BG
215chain DG
116chain BX
216chain DX
117chain BA
217chain DA
118chain BZ
218chain DZ
119(chain AV and resid 1 through 75)
219chain AW
319(chain CV and resid 1 through 75)
419chain CW
120chain AR
220chain CR
121chain AT
221chain CT
122chain BC
222chain DC
123chain BT
223chain DT
124chain B6
224chain D6
125chain AJ
225chain CJ
126chain AL
226chain CL
127chain BK
227chain DK
128chain BE
228chain DE
129chain B0
229chain D0
130chain B2
230chain D2
131chain AN
231chain CN
132chain AE
232chain CE
133chain AG
233chain CG
134chain B5
234chain D5
135chain BN
235chain DN
136chain AI
236chain CI
137chain BV
237chain DV
138chain AA
238chain CA
139chain AX
239chain CX
140chain AC
240chain CC
141chain BP
241chain DP
142chain B9
242chain D9
143chain BR
243chain DR
144chain BF
244chain DF
145chain AQ
245chain CQ
146chain BU
246chain DU
147chain AS
247chain CS
148chain BB
248chain DB
149chain AK
249chain CK
150chain B7
250chain D7
151chain BH
251chain DH
152chain B1
252chain D1
153chain AM
253chain CM
154chain BY
254chain DY
155chain AO
255chain CO
156chain B3
256chain D3
157chain BD
257chain DD

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLUchain B8B8HA2 - 652 - 65
21PROPROGLUGLUchain D8D8OC2 - 652 - 65
12METMETALAALAchain AFAFF1 - 1011 - 101
22METMETALAALAchain CFCFMB1 - 1011 - 101
13METMETTRPTRPchain AHAHH1 - 1381 - 138
23METMETTRPTRPchain CHCHOB1 - 1381 - 138
14METMETLEULEUchain BOBOVA1 - 1221 - 122
24METMETLEULEUchain DODOCD1 - 1221 - 122
15METMETALAALAchain BIBIRA1 - 1461 - 146
25METMETALAALAchain DIDIYC1 - 1461 - 146
16VALVALHISHISchain B4B4DA10 - 4010 - 40
26VALVALHISHISchain D4D4KC10 - 4010 - 40
17METMETLYSLYSchain BWBWDB1 - 1131 - 113
27METMETLYSLYSchain DWDWKD1 - 1131 - 113
18GLYGLYLYSLYSchain AUAUU2 - 262 - 26
28GLYGLYLYSLYSchain CUCUBC2 - 262 - 26
19METMETGLNGLNchain BQBQXA1 - 1411 - 141
29METMETGLNGLNchain DQDQED1 - 1411 - 141
110VALVALGLUGLUchain ABABB7 - 2417 - 241
210VALVALGLUGLUchain CBCBIB7 - 2417 - 241
111GLYGLYARGARGchain ADADD2 - 2092 - 209
211GLYGLYARGARGchain CDCDKB2 - 2092 - 209
112LYSLYSGLYGLYchain BSBSZA11 - 10911 - 109
212LYSLYSGLYGLYchain DSDSGD11 - 10911 - 109
113LEULEUARGARGchain AYAYY6 - 3567 - 357
213LEULEUARGARGchain CYCYFC6 - 3567 - 357
114METMETALAALAchain APAPP1 - 841 - 84
214METMETALAALAchain CPCPWB1 - 841 - 84
115PROPROLYSLYSchain BGBGPA2 - 1822 - 182
215PROPROLYSLYSchain DGDGWC2 - 1822 - 182
116THRTHRLEULEUchain BXBXEB3 - 953 - 95
216THRTHRLEULEUchain DXDXLD3 - 953 - 95
117AAUUchain BABAJA6 - 28976 - 2906
217AAUUchain DADAQC6 - 28976 - 2906
118TYRTYRALAALAchain BZBZGB3 - 1873 - 187
218TYRTYRALAALAchain DZDZND3 - 1873 - 187
119GGCC(chain AV and resid 1 through 75)AVV1 - 751 - 75
219GGCCchain AWAWW1 - 751 - 75
319GGCC(chain CV and resid 1 through 75)CVCC1 - 751 - 75
419GGCCchain CWCWDC1 - 751 - 75
120LYSLYSLYSLYSchain ARARR19 - 8819 - 88
220LYSLYSLYSLYSchain CRCRYB19 - 8819 - 88
121ARGARGALAALAchain ATATT8 - 1068 - 106
221ARGARGALAALAchain CTCTAC8 - 1068 - 106
122PROPROSERSERchain BCBCLA2 - 2292 - 229
222PROPROSERSERchain DCDCSC2 - 2292 - 229
123METMETALAALAchain BTBTAB1 - 1381 - 138
223METMETALAALAchain DTDTHD1 - 1381 - 138
124LEULEULYSLYSchain B6B6FA9 - 539 - 53
224LEULEULYSLYSchain D6D6MC9 - 539 - 53
125LYSLYSVALVALchain AJAJJ3 - 1013 - 101
225LYSLYSVALVALchain CJCJQB3 - 1013 - 101
126PROPROALAALAchain ALALL5 - 1292 - 126
226PROPROALAALAchain CLCLSB5 - 1292 - 126
127METMETALAALAchain BKBKTA1 - 1411 - 141
227METMETALAALAchain DKDKAD1 - 1411 - 141
128METMETALAALAchain BEBENA1 - 2051 - 205
228METMETALAALAchain DEDEUC1 - 2051 - 205
129HISHISALAALAchain B0B0Z3 - 853 - 85
229HISHISALAALAchain D0D0GC3 - 853 - 85
130LYSLYSALAALAchain B2B2BA2 - 722 - 72
230LYSLYSALAALAchain D2D2IC2 - 722 - 72
131ALAALATRPTRPchain ANANN2 - 612 - 61
231ALAALATRPTRPchain CNCNUB2 - 612 - 61
132ASPASPGLUGLUchain AEAEE5 - 1555 - 155
232ASPASPGLUGLUchain CECELB5 - 1555 - 155
133ALAALATRPTRPchain AGAGG2 - 1562 - 156
233ALAALATRPTRPchain CGCGNB2 - 1562 - 156
134ALAALAVALVALchain B5B5EA2 - 602 - 60
234ALAALAVALVALchain D5D5LC2 - 602 - 60
135METMETGLUGLUchain BNBNUA1 - 1391 - 139
235METMETGLUGLUchain DNDNBD1 - 1391 - 139
136GLUGLUARGARGchain AIAII2 - 1282 - 128
236GLUGLUARGARGchain CICIPB2 - 1282 - 128
137METMETGLYGLYchain BVBVCB1 - 1011 - 101
237METMETGLYGLYchain DVDVJD1 - 1011 - 101
138UUAAchain AAAAA5 - 15316 - 1509
238UUAAchain CACAHB5 - 15316 - 1509
139AAAAchain AXAXX14 - 2114 - 21
239AAAAchain CXCXEC14 - 2114 - 21
140GLYGLYILEILEchain ACACC2 - 2082 - 208
240GLYGLYILEILEchain CCCCJB2 - 2082 - 208
141ASPASPALAALAchain BPBPWA5 - 1505 - 150
241ASPASPALAALAchain DPDPDD5 - 1505 - 150
142LYSLYSGLYGLYchain B9B9IA2 - 372 - 37
242LYSLYSGLYGLYchain D9D9PC2 - 372 - 37
143ARGARGGLUGLUchain BRBRYA2 - 1182 - 118
243ARGARGGLUGLUchain DRDRFD2 - 1182 - 118
144METMETGLYGLYchain BFBFOA1 - 2081 - 208
244METMETGLYGLYchain DFDFVC1 - 2081 - 208
145PROPROARGARGchain AQAQQ2 - 1012 - 101
245PROPROARGARGchain CQCQXB2 - 1012 - 101
146PROPROGLYGLYchain BUBUBB2 - 1182 - 118
246PROPROGLYGLYchain DUDUID2 - 1182 - 118
147SERSERGLYGLYchain ASASS4 - 824 - 82
247SERSERGLYGLYchain CSCSZB4 - 824 - 82
148UUGGchain BBBBKA1 - 1191 - 119
248UUGGchain DBDBRC1 - 1191 - 119
149LYSLYSSERSERchain AKAKK11 - 12911 - 129
249LYSLYSSERSERchain CKCKRB11 - 12911 - 129
150METMETARGARGchain B7B7GA1 - 491 - 49
250METMETARGARGchain D7D7NC1 - 491 - 49
151LEULEULEULEUchain BHBHQA7 - 1717 - 171
251LEULEULEULEUchain DHDHXC7 - 1717 - 171
152LYSLYSLYSLYSchain B1B1AA3 - 963 - 96
252LYSLYSLYSLYSchain D1D1HC3 - 963 - 96
153ALAALALYSLYSchain AMAMM2 - 1262 - 126
253ALAALALYSLYSchain CMCMTB2 - 1262 - 126
154ARGARGCYSCYSchain BYBYFB2 - 1022 - 102
254ARGARGCYSCYSchain DYDYMD2 - 1022 - 102
155PROPROGLYGLYchain AOAOO2 - 892 - 89
255PROPROGLYGLYchain COCOVB2 - 892 - 89
156METMETGLUGLUchain B3B3CA1 - 601 - 60
256METMETGLUGLUchain D3D3JC1 - 601 - 60
157ALAALAARGARGchain BDBDMA2 - 2742 - 274
257ALAALAARGARGchain DDDDTC2 - 2742 - 274

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57

-
Components

-
RNA chain , 5 types, 12 molecules AACAAVAWCVCWAXCXBADABBDB

#1: RNA chain 16S rRNA /


Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076
#22: RNA chain
E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)


Mass: 24485.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1315725308
#23: RNA chain mRNA / Messenger RNA


Mass: 8132.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#35: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 947935.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 37223181
#36: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 37223181

-
30S ribosomal protein ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...

#2: Protein 30S ribosomal protein S2 /


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62662
#3: Protein 30S ribosomal protein S3 /


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62663
#4: Protein 30S ribosomal protein S4 /


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62664
#5: Protein 30S ribosomal protein S5 /


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27152
#6: Protein 30S ribosomal protein S6 /


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23370
#7: Protein 30S ribosomal protein S7 /


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62667
#8: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24319
#9: Protein 30S ribosomal protein S9 /


Mass: 14429.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62669
#10: Protein 30S ribosomal protein S10 /


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80375
#11: Protein 30S ribosomal protein S11 /


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62654
#12: Protein 30S ribosomal protein S12 /


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17293
#13: Protein 30S ribosomal protein S13 /


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62655
#14: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320
#15: Protein 30S ribosomal protein S15 /


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80378
#16: Protein 30S ribosomal protein S16 /


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62238
#17: Protein 30S ribosomal protein S17 /


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P0DOY7
#18: Protein 30S ribosomal protein S18 /


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62659
#19: Protein 30S ribosomal protein S19 /


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381
#20: Protein 30S ribosomal protein S20 /


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / Ribosome


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62612

-
Protein , 1 types, 2 molecules AYCY

#24: Protein Peptide chain release factor 2


Mass: 40700.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: prfB, Ththe16_0244 / Production host: Escherichia coli (E. coli) / References: UniProt: F6DD48

+
50S ribosomal protein ... , 32 types, 64 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...

#25: Protein 50S ribosomal protein L27 /


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60493
#26: Protein 50S ribosomal protein L28 /


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60494
#27: Protein 50S ribosomal protein L29 /


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72I12
#28: Protein 50S ribosomal protein L30 /


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P74909
#29: Protein 50S ribosomal protein L31 /


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72JR0
#30: Protein 50S ribosomal protein L32 /


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80339
#31: Protein 50S ribosomal protein L33 /


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72GW3
#32: Protein/peptide 50S ribosomal protein L34 /


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80340
#33: Protein 50S ribosomal protein L35 /


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80341
#34: Protein/peptide 50S ribosomal protein L36 /


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80256
#37: Protein 50S ribosomal protein L1 /


Mass: 24872.721 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP7
#38: Protein 50S ribosomal protein L2 /


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72I07
#39: Protein 50S ribosomal protein L3 /


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P52860
#40: Protein 50S ribosomal protein L4 /


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN9
#41: Protein 50S ribosomal protein L5 /


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P41201
#42: Protein 50S ribosomal protein L6 /


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24316
#43: Protein 50S ribosomal protein L9 /


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLQ1
#44: Protein 50S ribosomal protein L10 /


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#45: Protein 50S ribosomal protein L11 /


Mass: 15526.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P36238
#46: Protein 50S ribosomal protein L13 /


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72IN1
#47: Protein 50S ribosomal protein L14 /


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHP8
#48: Protein 50S ribosomal protein L15 /


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P74910
#49: Protein 50S ribosomal protein L16 /


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60489
#50: Protein 50S ribosomal protein L17 /


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72I33
#51: Protein 50S ribosomal protein L18 /


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80320
#52: Protein 50S ribosomal protein L19 /


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P60490
#53: Protein 50S ribosomal protein L20 /


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72L76
#54: Protein 50S ribosomal protein L21 /


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72HR2
#55: Protein 50S ribosomal protein L22 /


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P48286
#56: Protein 50S ribosomal protein L23 /


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q9RA57
#57: Protein 50S ribosomal protein L24 /


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q56435
#58: Protein 50S ribosomal protein L25 /


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q72IA7

-
Non-polymers , 3 types, 499 molecules

#59: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 474 / Source method: obtained synthetically / Formula: Mg
#60: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#61: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mM HEPES, pH 7.5, 10 mM magnesium acetate, 50 mM potassium chloride, 10 mM ammonium chloride, 6 mM BME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2017
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 970373 / % possible obs: 100 % / Redundancy: 41.9 % / Biso Wilson estimate: 128.73 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.439 / Net I/σ(I): 10.29
Reflection shellResolution: 3.2→3.25 Å / Redundancy: 29.8 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 43805 / CC1/2: 0.479 / Rrim(I) all: 3.111 / % possible all: 100

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4V5J

4v5j


Resolution: 3.2→48.981 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 28.5
RfactorNum. reflection% reflection
Rfree0.2474 48516 5 %
Rwork0.2229 --
obs0.2241 970343 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 509.47 Å2 / Biso mean: 160.6661 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.2→48.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms102488 201472 480 19 304459
Biso mean--76.03 64.49 -
Num. residues----22404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004329756
X-RAY DIFFRACTIONf_angle_d1.091492108
X-RAY DIFFRACTIONf_chiral_restr0.0562244
X-RAY DIFFRACTIONf_plane_restr0.00727518
X-RAY DIFFRACTIONf_dihedral_angle_d16.726177160
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B8621X-RAY DIFFRACTION4.929TORSIONAL
12D8621X-RAY DIFFRACTION4.929TORSIONAL
21AF1032X-RAY DIFFRACTION4.929TORSIONAL
22CF1032X-RAY DIFFRACTION4.929TORSIONAL
31AH1403X-RAY DIFFRACTION4.929TORSIONAL
32CH1403X-RAY DIFFRACTION4.929TORSIONAL
41BO1179X-RAY DIFFRACTION4.929TORSIONAL
42DO1179X-RAY DIFFRACTION4.929TORSIONAL
51BI1264X-RAY DIFFRACTION4.929TORSIONAL
52DI1264X-RAY DIFFRACTION4.929TORSIONAL
61B4260X-RAY DIFFRACTION4.929TORSIONAL
62D4260X-RAY DIFFRACTION4.929TORSIONAL
71BW1061X-RAY DIFFRACTION4.929TORSIONAL
72DW1061X-RAY DIFFRACTION4.929TORSIONAL
81AU264X-RAY DIFFRACTION4.929TORSIONAL
82CU264X-RAY DIFFRACTION4.929TORSIONAL
91BQ1383X-RAY DIFFRACTION4.929TORSIONAL
92DQ1383X-RAY DIFFRACTION4.929TORSIONAL
101AB2230X-RAY DIFFRACTION4.929TORSIONAL
102CB2230X-RAY DIFFRACTION4.929TORSIONAL
111AD2035X-RAY DIFFRACTION4.929TORSIONAL
112CD2035X-RAY DIFFRACTION4.929TORSIONAL
121BS871X-RAY DIFFRACTION4.929TORSIONAL
122DS871X-RAY DIFFRACTION4.929TORSIONAL
131AY3348X-RAY DIFFRACTION4.929TORSIONAL
132CY3348X-RAY DIFFRACTION4.929TORSIONAL
141AP846X-RAY DIFFRACTION4.929TORSIONAL
142CP846X-RAY DIFFRACTION4.929TORSIONAL
151BG1539X-RAY DIFFRACTION4.929TORSIONAL
152DG1539X-RAY DIFFRACTION4.929TORSIONAL
161BX866X-RAY DIFFRACTION4.929TORSIONAL
162DX866X-RAY DIFFRACTION4.929TORSIONAL
171BA69616X-RAY DIFFRACTION4.929TORSIONAL
172DA69616X-RAY DIFFRACTION4.929TORSIONAL
181BZ1722X-RAY DIFFRACTION4.929TORSIONAL
182DZ1722X-RAY DIFFRACTION4.929TORSIONAL
191AV3584X-RAY DIFFRACTION4.929TORSIONAL
192AW3584X-RAY DIFFRACTION4.929TORSIONAL
193CV3584X-RAY DIFFRACTION4.929TORSIONAL
194CW3584X-RAY DIFFRACTION4.929TORSIONAL
201AR716X-RAY DIFFRACTION4.929TORSIONAL
202CR716X-RAY DIFFRACTION4.929TORSIONAL
211AT973X-RAY DIFFRACTION4.929TORSIONAL
212CT973X-RAY DIFFRACTION4.929TORSIONAL
221BC1160X-RAY DIFFRACTION4.929TORSIONAL
222DC1160X-RAY DIFFRACTION4.929TORSIONAL
231BT1299X-RAY DIFFRACTION4.929TORSIONAL
232DT1299X-RAY DIFFRACTION4.929TORSIONAL
241B6372X-RAY DIFFRACTION4.929TORSIONAL
242D6372X-RAY DIFFRACTION4.929TORSIONAL
251AJ983X-RAY DIFFRACTION4.929TORSIONAL
252CJ983X-RAY DIFFRACTION4.929TORSIONAL
261AL1145X-RAY DIFFRACTION4.929TORSIONAL
262CL1145X-RAY DIFFRACTION4.929TORSIONAL
271BK1211X-RAY DIFFRACTION4.929TORSIONAL
272DK1211X-RAY DIFFRACTION4.929TORSIONAL
281BE1840X-RAY DIFFRACTION4.929TORSIONAL
282DE1840X-RAY DIFFRACTION4.929TORSIONAL
291B0824X-RAY DIFFRACTION4.929TORSIONAL
292D0824X-RAY DIFFRACTION4.929TORSIONAL
301B2588X-RAY DIFFRACTION4.929TORSIONAL
302D2588X-RAY DIFFRACTION4.929TORSIONAL
311AN590X-RAY DIFFRACTION4.929TORSIONAL
312CN590X-RAY DIFFRACTION4.929TORSIONAL
321AE1446X-RAY DIFFRACTION4.929TORSIONAL
322CE1446X-RAY DIFFRACTION4.929TORSIONAL
331AG1578X-RAY DIFFRACTION4.929TORSIONAL
332CG1578X-RAY DIFFRACTION4.929TORSIONAL
341B5566X-RAY DIFFRACTION4.929TORSIONAL
342D5566X-RAY DIFFRACTION4.929TORSIONAL
351BN1378X-RAY DIFFRACTION4.929TORSIONAL
352DN1378X-RAY DIFFRACTION4.929TORSIONAL
361AI1200X-RAY DIFFRACTION4.929TORSIONAL
362CI1200X-RAY DIFFRACTION4.929TORSIONAL
371BV901X-RAY DIFFRACTION4.929TORSIONAL
372DV901X-RAY DIFFRACTION4.929TORSIONAL
381AA36088X-RAY DIFFRACTION4.929TORSIONAL
382CA36088X-RAY DIFFRACTION4.929TORSIONAL
391AX184X-RAY DIFFRACTION4.929TORSIONAL
392CX184X-RAY DIFFRACTION4.929TORSIONAL
401AC1877X-RAY DIFFRACTION4.929TORSIONAL
402CC1877X-RAY DIFFRACTION4.929TORSIONAL
411BP1270X-RAY DIFFRACTION4.929TORSIONAL
412DP1270X-RAY DIFFRACTION4.929TORSIONAL
421B9377X-RAY DIFFRACTION4.929TORSIONAL
422D9377X-RAY DIFFRACTION4.929TORSIONAL
431BR1146X-RAY DIFFRACTION4.929TORSIONAL
432DR1146X-RAY DIFFRACTION4.929TORSIONAL
441BF1898X-RAY DIFFRACTION4.929TORSIONAL
442DF1898X-RAY DIFFRACTION4.929TORSIONAL
451AQ1010X-RAY DIFFRACTION4.929TORSIONAL
452CQ1010X-RAY DIFFRACTION4.929TORSIONAL
461BU1162X-RAY DIFFRACTION4.929TORSIONAL
462DU1162X-RAY DIFFRACTION4.929TORSIONAL
471AS712X-RAY DIFFRACTION4.929TORSIONAL
472CS712X-RAY DIFFRACTION4.929TORSIONAL
481BB2848X-RAY DIFFRACTION4.929TORSIONAL
482DB2848X-RAY DIFFRACTION4.929TORSIONAL
491AK1108X-RAY DIFFRACTION4.929TORSIONAL
492CK1108X-RAY DIFFRACTION4.929TORSIONAL
501B7556X-RAY DIFFRACTION4.929TORSIONAL
502D7556X-RAY DIFFRACTION4.929TORSIONAL
511BH1466X-RAY DIFFRACTION4.929TORSIONAL
512DH1466X-RAY DIFFRACTION4.929TORSIONAL
521B1879X-RAY DIFFRACTION4.929TORSIONAL
522D1879X-RAY DIFFRACTION4.929TORSIONAL
531AM1184X-RAY DIFFRACTION4.929TORSIONAL
532CM1184X-RAY DIFFRACTION4.929TORSIONAL
541BY858X-RAY DIFFRACTION4.929TORSIONAL
542DY858X-RAY DIFFRACTION4.929TORSIONAL
551AO928X-RAY DIFFRACTION4.929TORSIONAL
552CO928X-RAY DIFFRACTION4.929TORSIONAL
561B3610X-RAY DIFFRACTION4.929TORSIONAL
562D3610X-RAY DIFFRACTION4.929TORSIONAL
571BD2516X-RAY DIFFRACTION4.929TORSIONAL
572DD2516X-RAY DIFFRACTION4.929TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2-3.23640.38916050.38113050332108
3.2364-3.27440.38916050.37693048732092
3.2744-3.31430.389116100.3733058932199
3.3143-3.35630.375916070.36343054432151
3.3563-3.40040.373316100.36063059032200
3.4004-3.4470.377416060.35983051032116
3.447-3.49620.364516070.35163052132128
3.4962-3.54840.365616080.34583055432162
3.5484-3.60390.347616100.33933059732207
3.6039-3.66290.338616090.33323056232171
3.6629-3.72610.32816130.31753065332266
3.7261-3.79380.329516080.30773055332161
3.7938-3.86670.316816130.29753064632259
3.8667-3.94560.294316080.28053054832156
3.9456-4.03140.292116140.26483068132295
4.0314-4.12510.272516140.25683065132265
4.1251-4.22820.278716160.25183070332319
4.2282-4.34250.265616100.23573059932209
4.3425-4.47020.255716150.22673068032295
4.4702-4.61430.257116170.22473073232349
4.6143-4.77910.238916150.2153068632301
4.7791-4.97030.230316180.20933073732355
4.9703-5.19630.230416210.19993080232423
5.1963-5.46990.229316210.19233079532416
5.4699-5.81210.210316220.18833081732439
5.8121-6.260.214116260.19133089832524
6.26-6.88840.214416280.18793095032578
6.8884-7.88160.204816340.17973104632680
7.8816-9.91650.21516440.18263123732881
9.9165-48.98710.197216820.16973195633638

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