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- PDB-4v8x: Structure of Thermus thermophilus ribosome -

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Basic information

Entry
Database: PDB / ID: 4v8x
TitleStructure of Thermus thermophilus ribosome
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • (transfer RNA) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3'
  • 5S ribosomal RNA
  • BACTERIAL TOXIN YOEB
  • TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
KeywordsRIBOSOME / TOXIN-ANTITOXIN / RIBOSOME-DEPENDENT NUCLEASE / MRNA DEGRADATION / TRANSLATION REGULATION
Function / homology
Function and homology information


global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / RNA catabolic process / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / RNA catabolic process / regulation of growth / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity, producing 3'-phosphomonoesters / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / response to heat / transferase activity / endonuclease activity / tRNA binding / Hydrolases; Acting on ester bonds / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 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 ...Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 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 L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / 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 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 L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, 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 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Putative mRNA interferase YoeB / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Putative mRNA interferase YoeB / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bTHX / Toxin YoeB / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
THERMUS THERMOPHILUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsFeng, S. / Chen, Y. / Kamada, K. / Wang, H. / Tang, K. / Wang, M. / Gao, Y.G.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Yoeb-Ribosome Structure: A Canonical Rnase that Requires the Ribosome for its Specific Activity.
Authors: Feng, S. / Chen, Y. / Kamada, K. / Wang, H. / Tang, K. / Wang, M. / Gao, Y.
History
DepositionJul 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4BYB, 4BYC, 4BYD, 4BYE
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 27, 2016Group: Derived calculations
Revision 1.3Apr 4, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.pdbx_description / _entity.src_method
Revision 1.4Jan 10, 2024Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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.pdbx_ptnr2_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S ribosomal RNA
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: transfer RNA
AW: transfer RNA
AX: 5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3'
AY: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
AZ: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
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 ribosomal RNA
BB: 5S ribosomal RNA
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
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 ribosomal RNA
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: transfer RNA
CW: transfer RNA
CX: BACTERIAL TOXIN YOEB
CY: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
CZ: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
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 ribosomal RNA
DB: 5S ribosomal RNA
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
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)4,522,358829
Polymers4,504,913118
Non-polymers17,445711
Water0
1
AA: 16S ribosomal RNA
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: transfer RNA
AW: transfer RNA
AX: 5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3'
AY: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
AZ: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
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 ribosomal RNA
BB: 5S ribosomal RNA
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
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)2,263,643413
Polymers2,254,95759
Non-polymers8,686354
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S ribosomal RNA
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: transfer RNA
CW: transfer RNA
CX: BACTERIAL TOXIN YOEB
CY: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
CZ: TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM
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 ribosomal RNA
DB: 5S ribosomal RNA
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
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)2,258,715416
Polymers2,249,95659
Non-polymers8,759357
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.594, 455.434, 616.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 7 types, 12 molecules AACAAVAWCVCWAXBADABBDBCX

#1: RNA chain 16S ribosomal RNA /


Mass: 488391.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: 70S RIBOSOMES PURIFIED FROM T. THERMOPHILUS / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55771382
#22: RNA chain transfer RNA /


Mass: 24816.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
#23: RNA chain transfer RNA /


Mass: 24802.785 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
#24: RNA chain 5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3'


Mass: 8246.125 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHETIC MRNA WITH ANTI-SHINE DALGARNO SEQUENCE, AAA CODON IN E-SITE, AUG CODON IN P-SITE AND UAG CODON IN A-SITE. A-SITE NUCLEOTIDES HAVE A 2'O-METHOXY MODIFICATION
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#36: RNA chain 23S ribosomal RNA /


Mass: 926365.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55771382
#37: 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: HB8
#59: RNA chain BACTERIAL TOXIN YOEB


Mass: 3259.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)

-
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) / Strain: HB8 / References: UniProt: P80371
#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) / Strain: HB8 / References: UniProt: P80372
#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) / Strain: HB8 / References: UniProt: P80373
#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) / Strain: HB8 / References: UniProt: P27152, UniProt: Q5SHQ5
#6: Protein 30S RIBOSOMAL PROTEIN S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P23370, UniProt: Q5SLP8
#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) / Strain: HB8 / References: UniProt: P17291
#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: HB8
References: UniProt: P24319, UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#9: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80374
#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) / Strain: HB8 / References: UniProt: P80375, UniProt: Q5SHN7
#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) / Strain: HB8 / References: UniProt: P80376
#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) / Strain: HB8 / References: UniProt: P17293, UniProt: Q5SHN3
#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) / Strain: HB8 / References: UniProt: P80377
#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) / Strain: HB8
References: UniProt: P24320, UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#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) / Strain: HB8 / References: UniProt: P80378, UniProt: Q5SJ76
#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) / Strain: HB8 / References: UniProt: Q5SJH3
#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) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#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) / Strain: HB8 / References: UniProt: Q5SLQ0
#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) / Strain: HB8 / References: UniProt: P80381, UniProt: Q5SHP2
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: P62612, UniProt: Q5SIH3

-
Protein , 1 types, 4 molecules AYAZCYCZ

#25: Protein
TOXIN OF THE YOEB-YEFM TOXIN-ANTITOXIN SYSTEM / TOXIN RELE


Mass: 10233.658 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Gene: B1563, JW1555, RELE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: C4ZSA5, UniProt: C8UCW6, UniProt: P69348*PLUS

+
50S RIBOSOMAL PROTEIN ... , 31 types, 62 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...

#26: 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) / Strain: HB8 / References: UniProt: P60493
#27: 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) / Strain: HB8 / References: UniProt: P60494
#28: 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) / Strain: HB8 / References: UniProt: Q5SHP6
#29: 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) / Strain: HB8 / References: UniProt: Q5SHQ6
#30: 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) / Strain: HB8 / References: UniProt: Q5SJE1
#31: 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) / Strain: HB8 / References: UniProt: P80339
#32: 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) / Strain: HB8 / References: UniProt: P35871
#33: 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) / Strain: HB8 / References: UniProt: P80340
#34: 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) / Strain: HB8 / References: UniProt: Q5SKU1
#35: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / / RIBOSOMAL PROTEIN B


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHR2
#38: 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) / Strain: HB8 / References: UniProt: Q5SLP7
#39: 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) / Strain: HB8 / References: UniProt: P60405
#40: 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) / Strain: HB8 / References: UniProt: Q5SHN8
#41: Protein 50S RIBOSOMAL PROTEIN L4 / / L1E


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#42: 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) / Strain: HB8 / References: UniProt: Q5SHQ0
#43: 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) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#44: 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) / Strain: HB8 / References: UniProt: Q5SLQ1
#45: 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) / Strain: HB8
#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) / Strain: HB8 / References: UniProt: P60488
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: Q5SHQ7
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: Q9Z9H5
#51: Protein 50S RIBOSOMAL PROTEIN L18 / / TL24


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ4
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: P60491
#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) / Strain: HB8 / References: UniProt: P60492
#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) / Strain: HB8 / References: UniProt: Q5SHP3
#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) / Strain: HB8 / References: UniProt: Q5SHP0
#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) / Strain: HB8 / References: UniProt: Q5SHP9
#58: Protein 50S RIBOSOMAL PROTEIN L25 / / TL5


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHZ1

-
Non-polymers , 2 types, 711 molecules

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


Mass: 24.305 Da / Num. of mol.: 707 / Source method: obtained synthetically / Formula: Mg
#61: Chemical
ChemComp-ZN / ZINC ION


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.72 % / Description: NONE
Crystal growpH: 7.1
Details: 0.1 M TRIS-HAC PH 7.2, 0.2 M KSCN, 4.1%-4.3% (W/V) PEG 20K AND 4.1%-4.3% (W/V) PEG 550MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 842970 / % possible obs: 99.7 % / Observed criterion σ(I): 1.6 / Redundancy: 5.1 % / Biso Wilson estimate: 75.6 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.3
Reflection shellResolution: 3.35→3.4 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
CNSmodel building
CNS1.2refinement
CNSdata reduction
CNSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3KIQ,3KIR

3kiq
PDB Unreleased entry

3kir
PDB Unreleased entry


Resolution: 3.35→49.79 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 21486010.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 38866 4.6 %RANDOM
Rwork0.223 ---
obs0.223 842969 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.5056 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 117.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å20 Å20 Å2
2---3.68 Å20 Å2
3---8.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.35→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20551 35849 155 0 56555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.35→3.56 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 6880 4.9 %
Rwork0.32 132688 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION3PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5AA

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