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- PDB-4v83: Crystal structure of a complex containing domain 3 from the PSIV ... -

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Basic information

Entry
Database: PDB / ID: 4v83
TitleCrystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to the 70S ribosome.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • domain 3 of PSIC IGR IRES RNA
  • ribosomal RNA 16S
KeywordsRIBOSOME / 70S / IGR / IRES / PSIV / CrPV
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
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 L10 / : / : ...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 L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / 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 L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZhu, J. / Korostelev, A. / Costantino, D. / Noller, H.F. / Kieft, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
Authors: Zhu, J. / Korostelev, A. / Costantino, D.A. / Donohue, J.P. / Noller, H.F. / Kieft, J.S.
History
DepositionDec 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3PYN, 3PYO, 3PYQ, 3PYR
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_ref_seq_dif
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: ribosomal RNA 16S
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: domain 3 of PSIC IGR IRES RNA
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L10
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B1: 50S ribosomal protein L31
B2: 50S ribosomal protein L32
B3: 50S ribosomal protein L33
B4: 50S ribosomal protein L34
B5: 50S ribosomal protein L35
CA: ribosomal RNA 16S
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: domain 3 of PSIC IGR IRES RNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L10
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L28
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D1: 50S ribosomal protein L31
D2: 50S ribosomal protein L32
D3: 50S ribosomal protein L33
D4: 50S ribosomal protein L34
D5: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,313,0382767
Polymers4,248,198106
Non-polymers64,8402661
Water00
1
AA: ribosomal RNA 16S
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: domain 3 of PSIC IGR IRES RNA
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L10
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B1: 50S ribosomal protein L31
B2: 50S ribosomal protein L32
B3: 50S ribosomal protein L33
B4: 50S ribosomal protein L34
B5: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,152,6421224
Polymers2,124,09953
Non-polymers28,5431171
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: ribosomal RNA 16S
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: domain 3 of PSIC IGR IRES RNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L10
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L28
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D1: 50S ribosomal protein L31
D2: 50S ribosomal protein L32
D3: 50S ribosomal protein L33
D4: 50S ribosomal protein L34
D5: 50S ribosomal protein L35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,160,3961543
Polymers2,124,09953
Non-polymers36,2971490
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.940, 455.590, 618.020
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
11A
21C
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B*A6 - 2897
211chain D*0
112chain A* and not (chain AA or chain AV)0
212chain C* and not (chain CA or chain CV)0
113chain AA and resid 925:1391925 - 1391
213chain CA and resid 925:1391925 - 1391
114chain AA and not resid 925:13910
214chain CA and not resid 925:13910
115chain AV0
215chain CV0

NCS ensembles :
ID
1
2
3
4
5

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Components

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RNA chain , 4 types, 8 molecules AACAAVCVBADABBDB

#1: RNA chain ribosomal RNA 16S


Mass: 489042.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#22: RNA chain domain 3 of PSIC IGR IRES RNA


Mass: 11183.638 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27
#23: RNA chain 23S ribosomal RNA


Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#24: RNA chain 5S ribosomal RNA


Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1

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

#2: Protein 30S ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62662
#3: Protein 30S ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62663
#4: Protein 30S ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62664
#5: Protein 30S ribosomal protein S5


Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62665
#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) / Strain: HB27 / References: UniProt: P62666
#7: Protein 30S ribosomal protein S7


Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / 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) / Strain: HB27 / References: UniProt: P62668
#9: Protein 30S ribosomal protein S9


Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62669
#10: Protein 30S ribosomal protein S10


Mass: 11299.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62653
#11: Protein 30S ribosomal protein S11


Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62654
#12: Protein 30S ribosomal protein S12


Mass: 13804.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P61941
#13: Protein 30S ribosomal protein S13


Mass: 13237.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62655
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62656
#15: Protein 30S ribosomal protein S15


Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62657
#16: Protein 30S ribosomal protein S16


Mass: 9924.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62238
#17: Protein 30S ribosomal protein S17


Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62658
#18: Protein 30S ribosomal protein S18


Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62659
#19: Protein 30S ribosomal protein S19


Mass: 8949.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62660
#20: Protein 30S ribosomal protein S20


Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62661
#21: Protein/peptide 30S ribosomal protein Thx


Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62613

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50S ribosomal protein ... , 29 types, 58 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...

#25: Protein 50S ribosomal protein L2


Mass: 29828.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I07
#26: Protein 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I04
#27: Protein 50S ribosomal protein L4


Mass: 22487.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I05
#28: Protein 50S ribosomal protein L5


Mass: 20944.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I16
#29: Protein 50S ribosomal protein L6


Mass: 17363.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I19
#30: Protein 50S ribosomal protein L9


Mass: 16107.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72GV5
#31: Protein 50S ribosomal protein L10


Mass: 7330.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72GS1
#32: Protein 50S ribosomal protein L13


Mass: 15568.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72IN1
#33: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I14
#34: Protein 50S ribosomal protein L15


Mass: 15858.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I23
#35: Protein 50S ribosomal protein L16


Mass: 15348.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I11
#36: Protein 50S ribosomal protein L17


Mass: 13618.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I33
#37: Protein 50S ribosomal protein L18


Mass: 10941.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I20
#38: Protein 50S ribosomal protein L19


Mass: 16247.915 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72JU9
#39: Protein 50S ribosomal protein L20


Mass: 13500.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72L76
#40: 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) / Strain: HB27 / References: UniProt: Q72HR2
#41: Protein 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I09
#42: Protein 50S ribosomal protein L23


Mass: 10273.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I06
#43: Protein 50S ribosomal protein L24


Mass: 11078.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I15
#44: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 21150.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72IA7
#45: Protein 50S ribosomal protein L27


Mass: 8587.940 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72HR3
#46: Protein 50S ribosomal protein L28


Mass: 9884.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72G84
#47: Protein 50S ribosomal protein L29


Mass: 7457.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I12
#48: Protein 50S ribosomal protein L30


Mass: 6670.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I22
#49: Protein/peptide 50S ribosomal protein L31


Mass: 3278.860 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72JR0
#50: Protein 50S ribosomal protein L32


Mass: 5818.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62652
#51: Protein/peptide 50S ribosomal protein L33


Mass: 5473.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72GW3
#52: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P80340
#53: Protein 50S ribosomal protein L35


Mass: 7245.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72L77

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Non-polymers , 2 types, 2661 molecules

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


Mass: 24.305 Da / Num. of mol.: 2657 / Source method: obtained synthetically / Formula: Mg
#55: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 3.6-5% PEG20,000, 6-14% MPD, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.5→60 Å / Num. obs: 743704 / Biso Wilson estimate: 106.18 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.999 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 1.33 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 7381 0.99 %
Rwork0.2331 --
obs0.2334 743704 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.895 Å2 / ksol: 0.219 e/Å3
Displacement parametersBiso max: 428.94 Å2 / Biso mean: 149.8145 Å2 / Biso min: 32.26 Å2
Baniso -1Baniso -2Baniso -3
1--8.4553 Å20 Å2-0 Å2
2--15.6244 Å2-0 Å2
3----7.169 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19106 33108 2 0 52216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004305258
X-RAY DIFFRACTIONf_angle_d0.9456332
X-RAY DIFFRACTIONf_chiral_restr0.03957770
X-RAY DIFFRACTIONf_plane_restr0.00324870
X-RAY DIFFRACTIONf_dihedral_angle_d21.682147206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11AA88276X-RAY DIFFRACTIONPOSITIONAL0.018
12AC88276X-RAY DIFFRACTIONPOSITIONAL0.018
21AA19106X-RAY DIFFRACTIONPOSITIONAL0.01
22AB19106X-RAY DIFFRACTIONPOSITIONAL0.01
31AA9949X-RAY DIFFRACTIONPOSITIONAL0.01
32AB9949X-RAY DIFFRACTIONPOSITIONAL0.01
41AA22423X-RAY DIFFRACTIONPOSITIONAL0.014
42AB22423X-RAY DIFFRACTIONPOSITIONAL0.014
51AA736X-RAY DIFFRACTIONPOSITIONAL0.007
52AB736X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.53980.32522610.3256238742413597
3.5398-3.58140.34142580.3294241852444399
3.5814-3.62510.33022350.32582427924514100
3.6251-3.67090.33342260.32042441824644100
3.6709-3.71920.3182630.30972443424697100
3.7192-3.77020.30432490.29732436324612100
3.7702-3.8240.32842680.29532437824646100
3.824-3.88110.31312360.28342447724713100
3.8811-3.94170.30652300.2772444424674100
3.9417-4.00630.28222490.26362448324732100
4.0063-4.07530.29682250.26362446924694100
4.0753-4.14940.28322810.25692441324694100
4.1494-4.22920.29942200.25032450124721100
4.2292-4.31540.27372320.2392446824700100
4.3154-4.40920.26542520.22912452224774100
4.4092-4.51170.25012410.22672450924750100
4.5117-4.62450.25842290.2192447424703100
4.6245-4.74940.27642280.22092455724785100
4.7494-4.88910.26382240.21762455824782100
4.8891-5.04670.2672530.20912455124804100
5.0467-5.22690.22212540.19382450724761100
5.2269-5.43590.22942500.18922464924899100
5.4359-5.6830.22172520.1842455824810100
5.683-5.98220.22492340.18572466624900100
5.9822-6.35630.24272730.18782465224925100
6.3563-6.84590.21362240.18642474724971100
6.8459-7.53280.21112320.17972477825010100
7.5328-8.6180.21972650.19092483125096100
8.618-10.83950.22992740.20842500625280100
10.8395-50.00450.28792630.27012557225835100

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