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- PDB-4wpo: Crystal structure of the Thermus thermophilus 70S ribosome in com... -

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Basic information

Entry
Database: PDB / ID: 4wpo
TitleCrystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G in the pre-translocational state
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 32
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • A-site tRNA
  • E-site tRNA
  • P-site tRNA
  • mRNA
KeywordsRIBOSOME / EFG / Elongation / Translocation
Function / homology
Function and homology information


translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Ribosomal protein L1, bacterial-type / Elongation Factor G, domain II / Elongation Factor G, domain III / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Ribosomal protein L1, bacterial-type / Elongation Factor G, domain II / Elongation Factor G, domain III / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal protein L25, long-form / Elongation factor G C-terminus / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L10 / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / : / : / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Elongation factor Tu domain 2 / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 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 protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / 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, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / 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 L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein L20 signature. / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature.
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / IRON/SULFUR CLUSTER / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 ...GUANOSINE-5'-DIPHOSPHATE / : / IRON/SULFUR CLUSTER / : / : / 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 / 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 uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Elongation factor G / 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 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MC4100 (bacteria)
Thermus thermophilus (bacteria)
Thermus thermophilus HB8 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, J. / Gagnon, M.G. / Steitz, T.A.
CitationJournal: Cell / Year: 2015
Title: Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.
Authors: Lin, J. / Gagnon, M.G. / Bulkley, D. / Steitz, T.A.
History
DepositionOct 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / entity_src_nat ...entity_src_gen / entity_src_nat / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords
Revision 2.0Jul 3, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 23S Ribosomal RNA
AB: 5S Ribosomal RNA
AC: 50S ribosomal protein L1
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AK: 50S ribosomal protein L10
AL: 50S ribosomal protein L11
AN: 50S ribosomal protein L13
AO: 50S ribosomal protein L14
AP: 50S ribosomal protein L15
AQ: 50S ribosomal protein L16
AR: 50S ribosomal protein L17
AS: 50S ribosomal protein L18
AT: 50S ribosomal protein L19
AU: 50S ribosomal protein L20
AV: 50S ribosomal protein L21
AW: 50S ribosomal protein L22
AX: 50S ribosomal protein L23
AY: 50S ribosomal protein L24
AZ: 50S ribosomal protein L25
A0: 50S ribosomal protein L27
A1: 50S ribosomal protein L28
A2: 50S ribosomal protein L29
A3: 50S ribosomal protein L30
A4: 50S ribosomal protein L31
A5: 50S ribosomal protein L32
A6: 50S ribosomal protein L33
A7: 50S ribosomal protein L34
A8: 50S ribosomal protein L35
A9: 50S ribosomal protein L36
BA: 16S Ribosomal RNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14 type Z
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein Thx
BV: mRNA
BW: A-site tRNA
BX: P-site tRNA
BY: E-site tRNA
BZ: 50S ribosomal protein L9,Elongation factor G
CA: 23S Ribosomal RNA
CB: 5S Ribosomal RNA
CC: 50S ribosomal protein L1
CD: 50S ribosomal protein L2
CE: 50S ribosomal protein L3
CF: 50S ribosomal protein L4
CG: 50S ribosomal protein L5
CH: 50S ribosomal protein L6
CK: 50S ribosomal protein L10
CL: 50S ribosomal protein L11
CN: 50S ribosomal protein L13
CO: 50S ribosomal protein L14
CP: 50S ribosomal protein L15
CQ: 50S ribosomal protein L16
CR: 50S ribosomal protein L17
CS: 50S ribosomal protein L18
CT: 50S ribosomal protein L19
CU: 50S ribosomal protein L20
CV: 50S ribosomal protein L21
CW: 50S ribosomal protein L22
CX: 50S ribosomal protein L23
CY: 50S ribosomal protein L24
CZ: 50S ribosomal protein L25
C0: 50S ribosomal protein L27
C1: 50S ribosomal protein L28
C2: 50S ribosomal protein L29
C3: 50S ribosomal protein L30
C4: 50S ribosomal protein L31
C5: 50S ribosomal protein L32
C6: 50S ribosomal protein L33
C7: 50S ribosomal protein L34
C8: 50S ribosomal protein L35
C9: 50S ribosomal protein L36
DA: 16S Ribosomal RNA
DB: 30S ribosomal protein S2
DC: 30S ribosomal protein S3
DD: 30S ribosomal protein S4
DE: 30S ribosomal protein S5
DF: 30S ribosomal protein S6
DG: 30S ribosomal protein S7
DH: 30S ribosomal protein S8
DI: 30S ribosomal protein S9
DJ: 30S ribosomal protein S10
DK: 30S ribosomal protein S11
DL: 30S ribosomal protein S12
DM: 30S ribosomal protein S13
DN: 30S ribosomal protein S14 type Z
DO: 30S ribosomal protein S15
DP: 30S ribosomal protein S16
DQ: 30S ribosomal protein S17
DR: 30S ribosomal protein S18
DS: 30S ribosomal protein S19
DT: 30S ribosomal protein S20
DU: 30S ribosomal protein Thx
DV: mRNA
DW: A-site tRNA
DX: P-site tRNA
DY: E-site tRNA
DZ: 50S ribosomal protein L9,Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,806,7692191
Polymers4,754,385118
Non-polymers52,3852073
Water54,4053020
1
AA: 23S Ribosomal RNA
AB: 5S Ribosomal RNA
AC: 50S ribosomal protein L1
AD: 50S ribosomal protein L2
AE: 50S ribosomal protein L3
AF: 50S ribosomal protein L4
AG: 50S ribosomal protein L5
AH: 50S ribosomal protein L6
AK: 50S ribosomal protein L10
AL: 50S ribosomal protein L11
AN: 50S ribosomal protein L13
AO: 50S ribosomal protein L14
AP: 50S ribosomal protein L15
AQ: 50S ribosomal protein L16
AR: 50S ribosomal protein L17
AS: 50S ribosomal protein L18
AT: 50S ribosomal protein L19
AU: 50S ribosomal protein L20
AV: 50S ribosomal protein L21
AW: 50S ribosomal protein L22
AX: 50S ribosomal protein L23
AY: 50S ribosomal protein L24
AZ: 50S ribosomal protein L25
A0: 50S ribosomal protein L27
A1: 50S ribosomal protein L28
A2: 50S ribosomal protein L29
A3: 50S ribosomal protein L30
A4: 50S ribosomal protein L31
A5: 50S ribosomal protein L32
A6: 50S ribosomal protein L33
A7: 50S ribosomal protein L34
A8: 50S ribosomal protein L35
A9: 50S ribosomal protein L36
BA: 16S Ribosomal RNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14 type Z
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
BU: 30S ribosomal protein Thx
BV: mRNA
BW: A-site tRNA
BX: P-site tRNA
BY: E-site tRNA
BZ: 50S ribosomal protein L9,Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,406,6851231
Polymers2,377,19259
Non-polymers29,4931172
Water64936
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 23S Ribosomal RNA
CB: 5S Ribosomal RNA
CC: 50S ribosomal protein L1
CD: 50S ribosomal protein L2
CE: 50S ribosomal protein L3
CF: 50S ribosomal protein L4
CG: 50S ribosomal protein L5
CH: 50S ribosomal protein L6
CK: 50S ribosomal protein L10
CL: 50S ribosomal protein L11
CN: 50S ribosomal protein L13
CO: 50S ribosomal protein L14
CP: 50S ribosomal protein L15
CQ: 50S ribosomal protein L16
CR: 50S ribosomal protein L17
CS: 50S ribosomal protein L18
CT: 50S ribosomal protein L19
CU: 50S ribosomal protein L20
CV: 50S ribosomal protein L21
CW: 50S ribosomal protein L22
CX: 50S ribosomal protein L23
CY: 50S ribosomal protein L24
CZ: 50S ribosomal protein L25
C0: 50S ribosomal protein L27
C1: 50S ribosomal protein L28
C2: 50S ribosomal protein L29
C3: 50S ribosomal protein L30
C4: 50S ribosomal protein L31
C5: 50S ribosomal protein L32
C6: 50S ribosomal protein L33
C7: 50S ribosomal protein L34
C8: 50S ribosomal protein L35
C9: 50S ribosomal protein L36
DA: 16S Ribosomal RNA
DB: 30S ribosomal protein S2
DC: 30S ribosomal protein S3
DD: 30S ribosomal protein S4
DE: 30S ribosomal protein S5
DF: 30S ribosomal protein S6
DG: 30S ribosomal protein S7
DH: 30S ribosomal protein S8
DI: 30S ribosomal protein S9
DJ: 30S ribosomal protein S10
DK: 30S ribosomal protein S11
DL: 30S ribosomal protein S12
DM: 30S ribosomal protein S13
DN: 30S ribosomal protein S14 type Z
DO: 30S ribosomal protein S15
DP: 30S ribosomal protein S16
DQ: 30S ribosomal protein S17
DR: 30S ribosomal protein S18
DS: 30S ribosomal protein S19
DT: 30S ribosomal protein S20
DU: 30S ribosomal protein Thx
DV: mRNA
DW: A-site tRNA
DX: P-site tRNA
DY: E-site tRNA
DZ: 50S ribosomal protein L9,Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,400,084960
Polymers2,377,19259
Non-polymers22,892901
Water46826
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.890, 449.030, 622.900
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, 14 molecules AACAABCBBADABVDVBWDWBXDXBYDY

#1: RNA chain 23S Ribosomal RNA


Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#2: RNA chain 5S Ribosomal RNA


Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#34: RNA chain 16S Ribosomal RNA


Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: GenBank: 55771382
#55: RNA chain mRNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized mRNA / Source: (synth.) synthetic construct (others)
#56: RNA chain A-site tRNA


Mass: 24792.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Phenylalanine tRNA
Source: (gene. exp.) Escherichia coli str. K-12 substr. MC4100 (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 557270520
#57: RNA chain P-site tRNA


Mass: 25005.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Initiator Methionine tRNA
Source: (gene. exp.) Escherichia coli str. K-12 substr. MC4100 (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 557270520
#58: RNA chain E-site tRNA


Mass: 24645.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Phenylalanine tRNA
Source: (gene. exp.) Escherichia coli str. K-12 substr. MC4100 (bacteria)
Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600 / References: GenBank: 557270520

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50S ribosomal protein ... , 32 types, 64 molecules ACCCADCDAECEAFCFAGCGAHCHAKCKALCLANCNAOCOAPCPAQCQARCRASCSATCT...

#3: Protein 50S ribosomal protein L1


Mass: 24741.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP7
#4: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#5: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#6: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#7: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#8: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#9: Protein 50S ribosomal protein L10


Mass: 18586.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8VVE3
#10: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP6
#11: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#12: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#13: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#14: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#15: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#16: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#17: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#18: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#19: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#20: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#21: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#22: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#23: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#24: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#25: 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 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#26: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#27: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#28: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#29: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#30: 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 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#31: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#32: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#33: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2
#59: Protein 50S ribosomal protein L9,Elongation factor G / EF-G


Mass: 84416.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: a chimeric protein made of residues 1-74 of ribosomal protein L9 and residues 8-691 of elongation factor G
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rplI, TTHA0242, fusA, fus, TTHA1695 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SLQ1, UniProt: Q5SHN5

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

#35: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80371
#36: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80372
#37: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80373
#38: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5
#39: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8
#40: 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 / ATCC 27634 / DSM 579 / References: UniProt: P17291
#41: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#42: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80374
#43: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7
#44: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80376
#45: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3
#46: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#47: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#48: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76
#49: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3
#50: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#51: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0
#52: 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 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2
#53: 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 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#54: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

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Non-polymers , 6 types, 5093 molecules

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


Mass: 24.305 Da / Num. of mol.: 2056 / Source method: obtained synthetically / Formula: Mg
#61: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#62: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#63: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#64: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#65: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3020 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.6
Details: 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.6-3.0% PEG-20K, 7-10% MPD, 0.5mM BME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 1417921 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.08 % / Biso Wilson estimate: 54.72 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 14.48
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 7.24 % / Rmerge(I) obs: 1.488 / Mean I/σ(I) obs: 1.56 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.63 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 70965 5.02 %
Rwork0.202 --
obs0.205 1413694 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms104844 203367 2141 3020 313372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01337158
X-RAY DIFFRACTIONf_angle_d1.531502001
X-RAY DIFFRACTIONf_dihedral_angle_d16.833154566
X-RAY DIFFRACTIONf_chiral_restr0.0763103
X-RAY DIFFRACTIONf_plane_restr0.00728059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.455522840.423143725X-RAY DIFFRACTION97
2.8318-2.86510.448824200.409243676X-RAY DIFFRACTION98
2.8651-2.90010.426323390.390743827X-RAY DIFFRACTION98
2.9001-2.93680.420523340.374644025X-RAY DIFFRACTION98
2.9368-2.97540.397222980.358744096X-RAY DIFFRACTION98
2.9754-3.01620.386723630.339444172X-RAY DIFFRACTION98
3.0162-3.05920.369523510.324144295X-RAY DIFFRACTION99
3.0592-3.10490.35923210.309844409X-RAY DIFFRACTION99
3.1049-3.15340.327523190.282644496X-RAY DIFFRACTION99
3.1534-3.20510.315223570.267144592X-RAY DIFFRACTION99
3.2051-3.26040.313823000.257644686X-RAY DIFFRACTION99
3.2604-3.31960.290723220.239744736X-RAY DIFFRACTION99
3.3196-3.38350.286423100.231844851X-RAY DIFFRACTION99
3.3835-3.45250.266923920.222744648X-RAY DIFFRACTION100
3.4525-3.52760.273623490.217844780X-RAY DIFFRACTION100
3.5276-3.60960.250923640.205844772X-RAY DIFFRACTION99
3.6096-3.69980.251323990.199944786X-RAY DIFFRACTION100
3.6998-3.79980.241923690.18744894X-RAY DIFFRACTION100
3.7998-3.91160.233123010.177444974X-RAY DIFFRACTION100
3.9116-4.03780.225123480.17345012X-RAY DIFFRACTION100
4.0378-4.18210.220724530.171144843X-RAY DIFFRACTION100
4.1821-4.34940.215923690.164145091X-RAY DIFFRACTION100
4.3494-4.54720.206923850.158945058X-RAY DIFFRACTION100
4.5472-4.78680.203724110.15545054X-RAY DIFFRACTION100
4.7868-5.08640.20123950.148745172X-RAY DIFFRACTION100
5.0864-5.47870.194623900.139445200X-RAY DIFFRACTION100
5.4787-6.02920.197524460.139445329X-RAY DIFFRACTION100
6.0292-6.89960.206223900.144445406X-RAY DIFFRACTION100
6.8996-8.68520.205324730.149545632X-RAY DIFFRACTION100
8.6852-49.63460.219924130.18846492X-RAY DIFFRACTION99

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