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- PDB-4v9i: Crystal structure of thermus thermophilus 70S in complex with tRN... -

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Basic information

Entry
Database: PDB / ID: 4v9i
TitleCrystal structure of thermus thermophilus 70S in complex with tRNAs and mRNA containing a pseudouridine in a stop codon
Components
  • (30S Ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 32
  • (mRNA) x 2
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • A-SITE tRNA
  • E-SITE tRNA
  • P-SITE tRNA
KeywordsRIBOSOME / Ribosomal subunit / translation
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
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 L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19
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 ...: / : / 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 / 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 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / 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: 3.3 Å
AuthorsFernandez, I.S. / Ng, C.L. / Kelley, A.C. / Guowei, W. / Yu, Y.T. / Ramakrishnan, V.
CitationJournal: Nature / Year: 2013
Title: Unusual base pairing during the decoding of a stop codon by the ribosome.
Authors: Fernandez, I.S. / Ng, C.L. / Kelley, A.C. / Wu, G. / Yu, Y.T. / Ramakrishnan, V.
History
DepositionApr 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4K0L, 4K0M, 4K0P, 4K0Q
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands

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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
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: P-SITE tRNA
AW: E-SITE tRNA
AY: A-SITE tRNA
AX: mRNA
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L1
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BJ: 50S ribosomal protein L10
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
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
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: P-SITE tRNA
CW: E-SITE tRNA
CY: A-SITE tRNA
CX: mRNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DC: 50S Ribosomal protein L1
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: 50S ribosomal protein L10
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
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


Theoretical massNumber of molelcules
Total (without water)4,454,288116
Polymers4,454,288116
Non-polymers00
Water00
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
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: P-SITE tRNA
AW: E-SITE tRNA
AY: A-SITE tRNA
AX: mRNA
BA: 23S ribosomal RNA
BB: 5S ribosomal RNA
BC: 50S ribosomal protein L1
BD: 50S ribosomal protein L2
BE: 50S ribosomal protein L3
BF: 50S ribosomal protein L4
BG: 50S ribosomal protein L5
BH: 50S ribosomal protein L6
BI: 50S ribosomal protein L9
BJ: 50S ribosomal protein L10
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
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


Theoretical massNumber of molelcules
Total (without water)2,228,00158
Polymers2,228,00158
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S ribosomal RNA
CB: 30S Ribosomal protein S2
CC: 30S Ribosomal protein S3
CD: 30S Ribosomal protein S4
CE: 30S Ribosomal protein S5
CF: 30S Ribosomal protein S6
CG: 30S Ribosomal protein S7
CH: 30S Ribosomal protein S8
CI: 30S Ribosomal protein S9
CJ: 30S Ribosomal protein S10
CK: 30S Ribosomal protein S11
CL: 30S Ribosomal protein S12
CM: 30S Ribosomal protein S13
CN: 30S Ribosomal protein S14
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: P-SITE tRNA
CW: E-SITE tRNA
CY: A-SITE tRNA
CX: mRNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
DC: 50S Ribosomal protein L1
DD: 50S ribosomal protein L2
DE: 50S ribosomal protein L3
DF: 50S ribosomal protein L4
DG: 50S ribosomal protein L5
DH: 50S ribosomal protein L6
DI: 50S ribosomal protein L9
DJ: 50S ribosomal protein L10
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
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


Theoretical massNumber of molelcules
Total (without water)2,226,28758
Polymers2,226,28758
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.920, 449.900, 624.900
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 , 8 types, 14 molecules AACAAVCVAWCWAYCYAXBADABBDBCX

#1: RNA chain 16S ribosomal RNA


Mass: 488391.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382
#22: RNA chain P-SITE tRNA


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 443419838
#23: RNA chain E-SITE tRNA


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 443419838
#24: RNA chain A-SITE tRNA


Mass: 24430.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 443419838
#25: RNA chain mRNA


Mass: 2245.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#26: RNA chain 23S ribosomal RNA


Mass: 947919.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382
#27: RNA chain 5S ribosomal RNA


Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382
#59: RNA chain mRNA


Mass: 1241.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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

#2: Protein 30S Ribosomal protein S2


Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein 30S Ribosomal protein S3


Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein 30S Ribosomal protein S4


Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein 30S Ribosomal protein S5


Mass: 16331.079 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


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: 17919.775 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: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein 30S Ribosomal protein S10


Mass: 11299.176 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: 12606.369 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: 13804.311 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: 14078.486 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


Mass: 7027.529 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: 10447.213 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: 9924.469 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: 11722.904 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: 8155.812 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: 8949.435 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: 10921.086 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


Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

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50S ribosomal protein ... , 32 types, 62 molecules BCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBNDNBODOBPDPBQDQBRDRBSDSBTDTBU...

#28: Protein 50S ribosomal protein L1


Mass: 17813.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#29: Protein 50S ribosomal protein L2


Mass: 29828.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60405
#30: Protein 50S ribosomal protein L3


Mass: 22249.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN8
#31: Protein 50S ribosomal protein L4


Mass: 23014.670 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#32: Protein 50S ribosomal protein L5


Mass: 20930.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ0
#33: Protein 50S ribosomal protein L6


Mass: 17363.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#34: Protein 50S ribosomal protein L9


Mass: 16093.858 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ1
#35: Protein 50S ribosomal protein L10


Mass: 9258.110 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8
#36: Protein 50S ribosomal protein L13


Mass: 15699.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60488
#37: 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
#38: Protein 50S ribosomal protein L15


Mass: 15858.526 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ7
#39: 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
#40: Protein 50S ribosomal protein L17


Mass: 13618.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#41: Protein 50S ribosomal protein L18


Mass: 10941.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ4
#42: Protein 50S ribosomal protein L19


Mass: 16218.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60490
#43: Protein 50S ribosomal protein L20


Mass: 13571.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60491
#44: 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
#45: Protein 50S ribosomal protein L22


Mass: 12749.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP3
#46: Protein 50S ribosomal protein L23


Mass: 10273.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP0
#47: Protein 50S ribosomal protein L24


Mass: 11078.515 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP9
#48: Protein 50S ribosomal protein L25


Mass: 19892.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHZ1
#49: Protein 50S ribosomal protein L27


Mass: 9397.878 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60493
#50: Protein 50S ribosomal protein L28


Mass: 10458.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60494
#51: Protein 50S ribosomal protein L29


Mass: 8539.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP6
#52: Protein 50S ribosomal protein L30


Mass: 6670.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ6
#53: Protein/peptide 50S ribosomal protein L31


Mass: 3278.860 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJE1
#54: Protein 50S ribosomal protein L32


Mass: 6590.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80339
#55: Protein/peptide 50S ribosomal protein L33


Mass: 5473.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P35871
#56: Protein/peptide 50S ribosomal protein L34


Mass: 5975.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80340
#57: Protein 50S ribosomal protein L35


Mass: 7245.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKU1
#58: Protein/peptide 50S ribosomal protein L36


Mass: 4304.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHR2
#60: Protein 50S Ribosomal protein L1


Mass: 17103.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.87 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→39.57 Å / Num. all: 797158 / Num. obs: 132578 / % possible obs: 95.56 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.3→3.385 Å / % possible all: 87.42

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0031refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOLREPphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→39.57 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.823 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.868 / SU ML: 0.547 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 41956 5 %RANDOM
Rwork0.2254 ---
obs0.228 -95.56 %-
all-132578 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 412.18 Å2 / Biso mean: 92.8816 Å2 / Biso min: 19.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å2-0 Å2
2--1.5 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19157 37358 0 0 56515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013321205
X-RAY DIFFRACTIONr_bond_other_d0.0020.02191331
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.461480371
X-RAY DIFFRACTIONr_angle_other_deg1.2423449819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.109512005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40621.2734148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.7741518136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.415151332
X-RAY DIFFRACTIONr_chiral_restr0.1450.251637
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02221446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0274169
X-RAY DIFFRACTIONr_mcbond_it5.8919.29548347
X-RAY DIFFRACTIONr_mcbond_other5.899.29548346
X-RAY DIFFRACTIONr_mcangle_it9.93413.91460243
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 2803 -
Rwork0.329 53330 -
all-56133 -
obs--87.42 %

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