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- PDB-4v5j: Structure of the 70S ribosome bound to Release factor 2 and a sub... -

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Basic information

Entry
Database: PDB / ID: 4v5j
TitleStructure of the 70S ribosome bound to Release factor 2 and a substrate analog provides insights into catalysis of peptide release
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 32
  • 16S Ribosomal RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • E-SITE TRNA PHE OR P-SITE TRNA PHE (UNMODIFIED BASES)
  • MRNAMessenger RNA
  • PEPTIDE CHAIN RELEASE FACTOR 2
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / TRNA-BINDING / RRNA-BINDING / METAL-BINDING / ZINC-FINGER / TRANSLATION
Function / homology
Function and homology information


translation release factor activity, codon specific / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome ...translation release factor activity, codon specific / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / 5S rRNA binding / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / 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 ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / 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 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
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / 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 uS9 / 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 uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / 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 uL11 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Peptide chain release factor RF2 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
ESCHERICHIA COLI (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJin, H. / Kelley, A.C. / Loakes, D. / Ramakrishnan, V.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2010
Title: Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.
Authors: Jin, H. / Kelley, A.C. / Loakes, D. / Ramakrishnan, V.
History
DepositionMar 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2X9R, 2X9S, 2X9T, 2X9U
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity / pdbx_entity_src_syn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.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
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

Downloads & links

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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: 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 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
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 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: 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 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
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)4,650,6461218
Polymers4,623,664118
Non-polymers26,9821100
Water543
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: 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 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
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)2,325,347610
Polymers2,311,83259
Non-polymers13,515551
Water543
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: 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 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
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)2,325,299608
Polymers2,311,83259
Non-polymers13,467549
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.421, 452.497, 625.444
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 , 5 types, 12 molecules AACAAVAWCVCWAXCXBADABBDB

#1: RNA chain 16S Ribosomal RNA /


Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY.
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55979969
#22: RNA chain
E-SITE TRNA PHE OR P-SITE TRNA PHE (UNMODIFIED BASES)


Mass: 24615.730 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12
#23: RNA chain MRNA / Messenger RNA


Mass: 2495.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#35: RNA chain 23S RIBOSOMAL RNA /


Mass: 947935.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55979969
#36: RNA chain 5S RIBOSOMAL RNA /


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55979969

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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: 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: 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: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#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) / Strain: HB8 / 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) / Strain: HB8 / References: 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: 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 / 30S RIBOSOMAL PROTEIN S14


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*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: 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: A0A0N0BLS5*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: 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 / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

-
Protein , 1 types, 2 molecules AYCY

#24: Protein PEPTIDE CHAIN RELEASE FACTOR 2


Mass: 39857.273 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-369 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SM01

+
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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: P60494
#27: Protein 50S RIBOSOMAL PROTEIN L29 / / TL5


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
#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) / Strain: HB8 / References: UniProt: Q5SHQ6
#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) / Strain: HB8 / References: UniProt: Q5SJE1
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: P35871
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: Q5SKU1
#34: 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
#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) / Strain: HB8 / 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) / Strain: HB8 / References: UniProt: P60405
#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) / Strain: HB8 / References: UniProt: Q5SHN8
#40: 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
#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) / Strain: HB8 / References: UniProt: Q5SHQ0
#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) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#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) / Strain: HB8 / References: UniProt: Q5SLQ1
#44: Protein 50S RIBOSOMAL PROTEIN L10 /


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8
#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) / Strain: HB8 / References: UniProt: Q5SLP6
#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 , 3 types, 1103 molecules

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


Mass: 24.305 Da / Num. of mol.: 1094 / 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.: 3 / 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: 3.24 Å3/Da / Density % sol: 61.98 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE SELMER ET AL., SCIENCE 2006, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986
DetectorType: MARRESEARCH / Detector: CCD / Date: May 31, 2009 / Details: MIRROR
RadiationMonochromator: DYNAMICALLY BENDABLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 1071522 / % possible obs: 99.9 % / Observed criterion σ(I): 1.94 / Redundancy: 8.85 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.42
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.94 / % possible all: 100

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Processing

Software
NameVersionClassification
CNSmodel building
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J00

2j00
PDB Unreleased entry


Resolution: 3.1→47.86 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 20060710.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THIS IS THE FIRST OF A FOUR-PART DEPOSITION FOR A COMPLEX OF THE 70S RIBOSOME AND RELEASE FACTOR RF2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 47139 4.4 %RANDOM
Rwork0.223 ---
obs0.223 1071522 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4605 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 89.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2--1.75 Å20 Å2
3---0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.1→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21958 35754 551 3 58266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.49
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: RESTRAINS
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 8780 4.9 %
Rwork0.311 168763 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PAR_LIGAND.PARPAR_LIGAND.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA-MULTI-ENDO_NHA.PARAMDNA-RNA-MULTI-ENDO_NHA.TOP
X-RAY DIFFRACTION4PROTEIN_REP_NHA.PARAMPROTEIN_NHA.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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