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- PDB-4v9n: Crystal structure of the 70S ribosome bound with the Q253P mutant... -

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Basic information

Entry
Database: PDB / ID: 4v9n
TitleCrystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA (1504-MER)
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Bacterial peptide chain release factor 2 (RF-2)
  • P-site tRNA-fMet
  • messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
KeywordsRIBOSOME / Release factor 2 mutant
Function / homology
Function and homology information


translation release factor activity, codon specific / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit ...translation release factor activity, codon specific / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / 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 / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...Peptide chain release factor 2 / Peptide chain release factor / PCRF domain / PCRF / Peptide chain release factor class I superfamily / Prokaryotic-type class I peptide chain release factors signature. / Peptide chain release factor class I / RF-1 domain / 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 L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein 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 L11, N-terminal / Ribosomal protein L11, N-terminal domain / 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, RNA binding domain / Ribosomal protein L11/L12 / 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 S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature.
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein bTHX ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein bTHX / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL28 / Peptide chain release factor 2 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSantos, N. / Zhu, J. / Donohue, J.P. / Korostelev, A.A. / Noller, H.F.
CitationJournal: Structure / Year: 2013
Title: Crystal Structure of the 70S Ribosome Bound with the Q253P Mutant Form of Release Factor RF2.
Authors: Santos, N. / Zhu, J. / Donohue, J.P. / Korostelev, A.A. / Noller, H.F.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4KFH, 4KFI, 4KFK, 4KFL
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S rRNA (1504-MER)
AV: messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
AW: P-site tRNA-fMet
AY: Bacterial peptide chain release factor 2 (RF-2)
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
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
BK: 50S ribosomal protein L11
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
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
CA: 16S rRNA (1504-MER)
CV: messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
CW: P-site tRNA-fMet
CY: Bacterial peptide chain release factor 2 (RF-2)
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
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
DK: 50S ribosomal protein L11
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,435,8502524
Polymers4,377,013110
Non-polymers58,8372414
Water00
1
AA: 16S rRNA (1504-MER)
AV: messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
AW: P-site tRNA-fMet
AY: Bacterial peptide chain release factor 2 (RF-2)
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
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
BK: 50S ribosomal protein L11
BN: 50S ribosomal protein L13
BO: 50S ribosomal protein L14
BP: 50S ribosomal protein L15
BQ: 50S ribosomal protein L16
BR: 50S ribosomal protein L17
BS: 50S ribosomal protein L18
BT: 50S ribosomal protein L19
BU: 50S ribosomal protein L20
BV: 50S ribosomal protein L21
BW: 50S ribosomal protein L22
BX: 50S ribosomal protein L23
BY: 50S ribosomal protein L24
BZ: 50S ribosomal protein L25
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,219,8451341
Polymers2,188,50655
Non-polymers31,3381286
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S rRNA (1504-MER)
CV: messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
CW: P-site tRNA-fMet
CY: Bacterial peptide chain release factor 2 (RF-2)
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
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
DK: 50S ribosomal protein L11
DN: 50S ribosomal protein L13
DO: 50S ribosomal protein L14
DP: 50S ribosomal protein L15
DQ: 50S ribosomal protein L16
DR: 50S ribosomal protein L17
DS: 50S ribosomal protein L18
DT: 50S ribosomal protein L19
DU: 50S ribosomal protein L20
DV: 50S ribosomal protein L21
DW: 50S ribosomal protein L22
DX: 50S ribosomal protein L23
DY: 50S ribosomal protein L24
DZ: 50S ribosomal protein L25
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,216,0051183
Polymers2,188,50655
Non-polymers27,4981128
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.070, 454.400, 618.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 5 types, 10 molecules AACAAVCVAWCWBADABBDB

#1: RNA chain 16S rRNA (1504-MER)


Mass: 488431.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#2: RNA chain messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')


Mass: 3217.021 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27
#3: RNA chain P-site tRNA-fMet


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: CP001509.3
#25: RNA chain 23S ribosomal RNA


Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1
#26: 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: HB27 / References: GenBank: AE017221.1

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Protein , 1 types, 2 molecules AYCY

#4: Protein Bacterial peptide chain release factor 2 (RF-2)


Mass: 40889.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C1852 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72GJ6

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

#5: 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: HB27 / References: UniProt: P62662
#6: 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: HB27 / References: UniProt: P62663
#7: 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: HB27 / References: UniProt: P62664
#8: Protein 30S ribosomal protein S5


Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62665
#9: 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: HB27 / References: UniProt: P62666
#10: 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: HB27 / References: UniProt: P62667
#11: 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: HB27 / References: UniProt: P62668
#12: 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: HB27 / References: UniProt: P62669
#13: 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: HB27 / References: UniProt: P62653
#14: Protein 30S ribosomal protein S11


Mass: 12014.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62654
#15: Protein 30S ribosomal protein S12


Mass: 13604.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P61941
#16: Protein 30S ribosomal protein S13


Mass: 13308.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62655
#17: 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: HB27 / References: UniProt: P62656
#18: 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: HB27 / References: UniProt: P62657
#19: 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: HB27 / References: UniProt: P62238
#20: Protein 30S ribosomal protein S17


Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62658
#21: 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: HB27 / References: UniProt: P62659
#22: 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: HB27 / References: UniProt: P62660
#23: Protein 30S ribosomal protein S20


Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62661
#24: 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: HB27 / References: UniProt: P62613

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

#27: 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: HB27 / References: UniProt: Q72I07
#28: 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: HB27 / References: UniProt: Q72I04
#29: Protein 50S ribosomal protein L4


Mass: 22487.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I05
#30: Protein 50S ribosomal protein L5


Mass: 20944.428 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I16
#31: 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: HB27 / References: UniProt: Q72I19
#32: Protein 50S ribosomal protein L9


Mass: 16107.884 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72GV5
#33: 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: HB27 / References: UniProt: P62442
#34: Protein 50S ribosomal protein L13


Mass: 15568.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72IN1
#35: Protein 50S ribosomal protein L14


Mass: 13309.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I14
#36: 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: HB27 / References: UniProt: Q72I23
#37: Protein 50S ribosomal protein L16


Mass: 15148.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I11
#38: 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: HB27 / References: UniProt: Q72I33
#39: 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: HB27 / References: UniProt: Q72I20
#40: Protein 50S ribosomal protein L19


Mass: 16247.915 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72JU9
#41: Protein 50S ribosomal protein L20


Mass: 13648.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72L76
#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 (bacteria) / Strain: HB27 / References: UniProt: Q72HR2
#43: Protein 50S ribosomal protein L22


Mass: 12678.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I09
#44: 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: HB27 / References: UniProt: Q72I06
#45: 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: HB27 / References: UniProt: Q72I15
#46: Protein 50S ribosomal protein L25


Mass: 21021.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72IA7
#47: Protein 50S ribosomal protein L27


Mass: 8587.940 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72HR3
#48: Protein 50S ribosomal protein L28


Mass: 9884.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72G84
#49: Protein 50S ribosomal protein L29


Mass: 7457.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72I12
#50: 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: HB27 / References: UniProt: Q72I22
#51: 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: HB27 / References: UniProt: Q72JR0
#52: Protein 50S ribosomal protein L32


Mass: 5818.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62652
#53: 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: HB27 / References: UniProt: Q72GW3
#54: 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: HB27 / References: UniProt: P80340
#55: 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: HB27 / References: UniProt: Q72L77

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Non-polymers , 2 types, 2414 molecules

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


Mass: 24.305 Da / Num. of mol.: 2410 / Source method: obtained synthetically / Formula: Mg
#57: Chemical
ChemComp-ZN / ZINC ION


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

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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: 5

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.17 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL7-111.03322
SYNCHROTRONALS 12.3.121.116
SYNCHROTRONSSRL BL9-130.9636
SYNCHROTRONSSRL BL11-141.03316
Detector
IDDate
1Aug 2, 2012
2Feb 12, 2012
3Feb 29, 2012
4Dec 16, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
11.033221
21.1161
30.96361
41.033161
ReflectionResolution: 3.4→50 Å / Num. obs: 807927 / Redundancy: 7 %

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
CNSrefinement
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F1G AND 3F1H

3f1g
PDB Unreleased entry

3f1h
PDB Unreleased entry


Resolution: 3.4→49.672 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 16161 2 %RANDOM
Rwork0.2343 ---
obs0.235 807927 99.65 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.108 Å2 / ksol: 0.266 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5525 Å20 Å2-0 Å2
2--14.5549 Å2-0 Å2
3----11.0024 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21929 34186 1285 0 57400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004316343
X-RAY DIFFRACTIONf_angle_d0.621471736
X-RAY DIFFRACTIONf_dihedral_angle_d18.745171400
X-RAY DIFFRACTIONf_chiral_restr0.05359678
X-RAY DIFFRACTIONf_plane_restr0.00326360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.37625360.352326265X-RAY DIFFRACTION100
3.4386-3.47910.36635360.344826286X-RAY DIFFRACTION100
3.4791-3.52150.3685360.337126265X-RAY DIFFRACTION100
3.5215-3.56610.33935350.32326169X-RAY DIFFRACTION100
3.5661-3.6130.36385360.327926303X-RAY DIFFRACTION100
3.613-3.66240.33985370.310826289X-RAY DIFFRACTION100
3.6624-3.71470.32265370.298126336X-RAY DIFFRACTION100
3.7147-3.77020.31775360.293126249X-RAY DIFFRACTION100
3.7702-3.82910.30525370.279826305X-RAY DIFFRACTION100
3.8291-3.89180.30785360.26926288X-RAY DIFFRACTION100
3.8918-3.95890.29365380.261826338X-RAY DIFFRACTION100
3.9589-4.03090.29455340.260126158X-RAY DIFFRACTION99
4.0309-4.10830.3035330.254826147X-RAY DIFFRACTION99
4.1083-4.19220.28515390.240226388X-RAY DIFFRACTION100
4.1922-4.28330.27735380.232926381X-RAY DIFFRACTION100
4.2833-4.38290.25685370.222326303X-RAY DIFFRACTION100
4.3829-4.49240.28365390.228326417X-RAY DIFFRACTION100
4.4924-4.61380.2495380.220326363X-RAY DIFFRACTION100
4.6138-4.74940.24935380.210926362X-RAY DIFFRACTION100
4.7494-4.90260.25375380.207526355X-RAY DIFFRACTION100
4.9026-5.07770.23945400.204426457X-RAY DIFFRACTION100
5.0777-5.28070.23215400.196826477X-RAY DIFFRACTION100
5.2807-5.52080.23615350.19126206X-RAY DIFFRACTION99
5.5208-5.81140.2325420.181726543X-RAY DIFFRACTION100
5.8114-6.17490.20585420.177926574X-RAY DIFFRACTION100
6.1749-6.65070.24425430.190726617X-RAY DIFFRACTION100
6.6507-7.3180.22935430.192526603X-RAY DIFFRACTION100
7.318-8.37260.23245390.196926380X-RAY DIFFRACTION99
8.3726-10.5320.23915490.210826893X-RAY DIFFRACTION100
10.532-49.67750.25095540.240427049X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -61.7107 Å / Origin y: 44.8464 Å / Origin z: 68.9478 Å
111213212223313233
T0.0148 Å20.0151 Å2-0.0541 Å2-0.1072 Å20.05 Å2--0.0678 Å2
L0.019 °20.0479 °20.0398 °2-0.208 °20.1375 °2--0.1259 °2
S0.0042 Å °-0.04 Å °0.0029 Å °-0.1039 Å °-0.0207 Å °0.0401 Å °-0.0854 Å °-0.0354 Å °0.0287 Å °
Refinement TLS groupSelection details: all

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