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- PDB-1vy5: Crystal structure of the Thermus thermophilus 70S ribosome in the... -

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Basic information

Entry
Database: PDB / ID: 1vy5
TitleCrystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S Ribosomal RNA
  • 23S Ribosomal RNA
  • 5S Ribosomal RNA
  • A-site tRNA
  • E-site tRNA
  • P-site tRNA
  • mRNA
KeywordsRIBOSOME / 70S / Translation / Peptydil Transfer Reaction / Proton Transfer Mechanism / Acylated tRNA
Function / homology
Function and homology information


large ribosomal subunit / 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 ...large ribosomal subunit / 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 / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...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 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 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. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / : / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L21 / Ribosomal protein S15, bacterial-type / Ribosomal protein L19 / Ribosomal protein L19
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 ...: / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / 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 / 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 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 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 / 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 HB8 (bacteria)
Thermus thermophilus (bacteria)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPolikanov, Y.S. / Steitz, T.A. / Innis, C.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
Authors: Polikanov, Y.S. / Steitz, T.A. / Innis, C.A.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
SupersessionDec 10, 2014ID: 4QCQ, 4QCR, 4QCS, 4QCT
Revision 1.3Dec 10, 2014Group: Other
Revision 1.4Dec 17, 2014Group: Other
Revision 1.5Jan 28, 2015Group: Other
Revision 1.6May 31, 2017Group: Database references
Revision 2.0Jul 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
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
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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: mRNA
AW: A-site tRNA
AX: P-site tRNA
AY: E-site tRNA
BA: 23S Ribosomal RNA
BB: 5S Ribosomal RNA
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
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
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
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: mRNA
CW: A-site tRNA
CX: P-site tRNA
CY: E-site tRNA
DA: 23S Ribosomal RNA
DB: 5S Ribosomal RNA
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,552,6812205
Polymers4,500,633112
Non-polymers52,0482093
Water55,1623062
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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: mRNA
AW: A-site tRNA
AX: P-site tRNA
AY: E-site tRNA
BA: 23S Ribosomal RNA
BB: 5S Ribosomal RNA
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,279,4151229
Polymers2,250,31656
Non-polymers29,0991173
Water61334
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: mRNA
CW: A-site tRNA
CX: P-site tRNA
CY: E-site tRNA
DA: 23S Ribosomal RNA
DB: 5S Ribosomal RNA
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,273,266976
Polymers2,250,31656
Non-polymers22,949920
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.320, 450.060, 622.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 7 types, 14 molecules AACAAVCVAWCWAXCXAYCYBADABBDB

#1: 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
#22: RNA chain mRNA


Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) Synthetic DNA (others)
#23: RNA chain A-site tRNA


Mass: 24923.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Phenylalanine tRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600
#24: RNA chain P-site tRNA


Mass: 24846.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Initiator Methionine tRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600
#25: 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 (E. coli) / Strain: MRE-600 / Production host: Escherichia coli (E. coli) / Strain (production host): MRE-600
#26: 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
#27: 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

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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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY9
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377
#14: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY6
#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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY7
#18: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380
#21: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3

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

#28: Protein 50S ribosomal protein L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60405
#29: Protein 50S ribosomal protein L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN8
#30: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN9
#31: Protein 50S ribosomal protein L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ0
#32: Protein 50S ribosomal protein L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P0DOY8
#33: Protein 50S ribosomal protein L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ1
#34: Protein 50S ribosomal protein L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60488
#35: Protein 50S ribosomal protein L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP8
#36: Protein 50S ribosomal protein L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ7
#37: Protein 50S ribosomal protein L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60489
#38: Protein 50S ribosomal protein L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q9Z9H5
#39: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ4
#40: Protein 50S ribosomal protein L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60490
#41: Protein 50S ribosomal protein L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60491
#42: Protein 50S ribosomal protein L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60492
#43: Protein 50S ribosomal protein L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP3
#44: Protein 50S ribosomal protein L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP0
#45: Protein 50S ribosomal protein L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP9
#46: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHZ1
#47: Protein 50S ribosomal protein L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60493
#48: Protein 50S ribosomal protein L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P60494
#49: Protein 50S ribosomal protein L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP6
#50: Protein 50S ribosomal protein L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ6
#51: Protein 50S ribosomal protein L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJE1
#52: Protein 50S ribosomal protein L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80339
#53: Protein 50S ribosomal protein L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P35871
#54: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80340
#55: Protein 50S ribosomal protein L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SKU1
#56: 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 (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHR2

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Non-polymers , 5 types, 5155 molecules

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


Mass: 24.305 Da / Num. of mol.: 2077 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#59: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#60: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#61: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3062 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.22 %
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, 2.5% PEG-20K, 7-12% MPD, 0.5mM BME, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2013 / Details: S/N 60-0112-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→255.92 Å / Num. all: 1881317 / Num. obs: 1803654 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 50.59 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.066 / Net I/σ(I): 8.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.55-2.620.0121.02367194118644185.6
2.62-2.690.0121.29459662123944191.9
2.69-2.770.0121.61465607122545193.3
2.77-2.850.0122.04460966120756194.6
2.85-2.940.0122.69447773118327195.6
2.94-3.050.0123.66420270114259195.5
3.05-3.160.0125.16426457111400196.4
3.16-3.290.0126.79440077108904197.9
3.29-3.440.0128.09425943105161198.4
3.44-3.610.0129.34407111101002198.9
3.61-3.80.01210.8536213894675197.4
3.8-4.030.01213.338639591144199.1
4.03-4.310.01215.136525885929199.4
4.31-4.660.01216.8633212780107199.2
4.66-5.10.01217.8128185572392197.5
5.1-5.70.01220.1628796166752199.1
5.7-6.580.01220.1224930458917199
6.58-8.060.01221.8919666548977196.9
8.06-11.40.01227.0716603738767198.6
11.4-255.920.012328469521052194.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→152.51 Å / FOM work R set: 0.7678 / SU ML: 0.48 / σ(F): 1.33 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2797 90439 5.02 %
Rwork0.2326 --
obs0.2349 1802040 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.16 Å2 / Biso mean: 61.44 Å2 / Biso min: 26.46 Å2
Refinement stepCycle: LAST / Resolution: 2.55→152.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms91181 200791 2107 3062 297141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005321946
X-RAY DIFFRACTIONf_angle_d0.989478994
X-RAY DIFFRACTIONf_chiral_restr0.04360363
X-RAY DIFFRACTIONf_plane_restr0.00525467
X-RAY DIFFRACTIONf_dihedral_angle_d16.674148037
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.5790.389625210.3474484255094682
2.579-2.60930.396527120.3444517205443287
2.6093-2.64110.382228670.3375533855625290
2.6411-2.67460.379628620.3326546165747892
2.6746-2.70980.374629310.3239548225775393
2.7098-2.74690.370828760.3205552175809393
2.7469-2.78610.364929540.3139558175877194
2.7861-2.82770.361429740.3091560895906394
2.8277-2.87190.365930670.3119562575932495
2.8719-2.9190.374230250.3211566515967696
2.919-2.96940.363629880.3108570556004396
2.9694-3.02340.347830310.2874570816011296
3.0234-3.08150.332229250.2753557675869294
3.0815-3.14440.313530370.2637576736071097
3.1444-3.21280.319430400.2622580986113898
3.2128-3.28750.309430360.2551582956133198
3.2875-3.36980.300430260.2495584266145298
3.3698-3.46090.298830720.2451587076177999
3.4609-3.56270.28331420.2364587586190099
3.5627-3.67770.284730880.2308589936208199
3.6777-3.80920.266330290.2217574876051697
3.8092-3.96170.265930300.2201591106214099
3.9617-4.1420.257831750.2147591296230499
4.142-4.36040.249431640.2074593246248899
4.3604-4.63360.247431640.2063591926235699
4.6336-4.99140.247330910.1935582746136597
4.9914-5.49370.233331610.187592486240999
5.4937-6.28870.22731840.1816594096259399
6.2887-7.92310.22531130.1787587106182397
7.9231-152.78370.219831540.1911598666302097

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