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- PDB-4v54: Crystal structure of the bacterial ribosome from Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 4v54
TitleCrystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF).
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • ribosome recycling factor
KeywordsRIBOSOME / RNA-protein complex
Function / homology
Function and homology information


stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / 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 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
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / 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 uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL25 / Ribosome-recycling factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBorovinskaya, M.A. / Pai, R.D. / Zhang, W. / Schuwirth, B.-S. / Holton, J.M. / Hirokawa, G. / Kaji, H. / Kaji, A. / Cate, J.H.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for aminoglycoside inhibition of bacterial ribosome recycling.
Authors: Borovinskaya, M.A. / Pai, R.D. / Zhang, W. / Schuwirth, B.S. / Holton, J.M. / Hirokawa, G. / Kaji, H. / Kaji, A. / Cate, J.H.
History
DepositionJun 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2QBD, 2QBE, 2QBF, 2QBG
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS PART OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE BIOLOGICAL UNIT CONSISTS OF TWO SUBUNITS. THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT.
Remark 400COMPOUND THIS FILE, 2QBD, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 2QBD, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS TWO 70S RIBOSOMES AND IS DEPOSITED UNDER: 70S RIBOSOME ONE: 2QBD (30S SUBUNIT), 2QBE (50S SUBUNIT) 70S RIBOSOME TWO: 2QBF (30S SUBUNIT), 2QBG (50S SUBUNIT)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 16S rRNA
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
AB: 30S ribosomal protein S2
AU: 30S ribosomal protein S21
BA: 5S rRNA
BB: 23S rRNA
BI: 50S ribosomal protein L11
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BK: 50S ribosomal protein L14
BP: 50S ribosomal protein L19
BE: 50S ribosomal protein L4
BY: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B4: 50S ribosomal protein L36
B1: 50S ribosomal protein L33
B3: 50S ribosomal protein L35
BV: 50S ribosomal protein L25
B2: 50S ribosomal protein L34
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BX: 50S ribosomal protein L29
BH: 50S ribosomal protein L9
BJ: 50S ribosomal protein L13
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BQ: 50S ribosomal protein L20
BS: 50S ribosomal protein L22
BU: 50S ribosomal protein L24
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BR: 50S ribosomal protein L21
BT: 50S ribosomal protein L23
BZ: 50S ribosomal protein L28
BW: 50S ribosomal protein L27
B6: ribosome recycling factor
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
CB: 30S ribosomal protein S2
CA: 16S rRNA
CU: 30S ribosomal protein S21
DA: 5S rRNA
DB: 23S rRNA
DI: 50S ribosomal protein L11
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DK: 50S ribosomal protein L14
DP: 50S ribosomal protein L19
DE: 50S ribosomal protein L4
DY: 50S ribosomal protein L30
D0: 50S ribosomal protein L32
D4: 50S ribosomal protein L36
D1: 50S ribosomal protein L33
D3: 50S ribosomal protein L35
DV: 50S ribosomal protein L25
D2: 50S ribosomal protein L34
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DX: 50S ribosomal protein L29
DH: 50S ribosomal protein L9
DJ: 50S ribosomal protein L13
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DQ: 50S ribosomal protein L20
DS: 50S ribosomal protein L22
DU: 50S ribosomal protein L24
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DR: 50S ribosomal protein L21
DT: 50S ribosomal protein L23
DZ: 50S ribosomal protein L28
DW: 50S ribosomal protein L27
D6: ribosome recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,337,309451
Polymers4,328,841106
Non-polymers8,467345
Water29,3101627
1
AA: 16S rRNA
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
AB: 30S ribosomal protein S2
AU: 30S ribosomal protein S21
BA: 5S rRNA
BB: 23S rRNA
BI: 50S ribosomal protein L11
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BK: 50S ribosomal protein L14
BP: 50S ribosomal protein L19
BE: 50S ribosomal protein L4
BY: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B4: 50S ribosomal protein L36
B1: 50S ribosomal protein L33
B3: 50S ribosomal protein L35
BV: 50S ribosomal protein L25
B2: 50S ribosomal protein L34
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BX: 50S ribosomal protein L29
BH: 50S ribosomal protein L9
BJ: 50S ribosomal protein L13
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BQ: 50S ribosomal protein L20
BS: 50S ribosomal protein L22
BU: 50S ribosomal protein L24
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BR: 50S ribosomal protein L21
BT: 50S ribosomal protein L23
BZ: 50S ribosomal protein L28
BW: 50S ribosomal protein L27
B6: ribosome recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,168,618224
Polymers2,164,42153
Non-polymers4,197171
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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
CB: 30S ribosomal protein S2
CA: 16S rRNA
CU: 30S ribosomal protein S21
DA: 5S rRNA
DB: 23S rRNA
DI: 50S ribosomal protein L11
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DK: 50S ribosomal protein L14
DP: 50S ribosomal protein L19
DE: 50S ribosomal protein L4
DY: 50S ribosomal protein L30
D0: 50S ribosomal protein L32
D4: 50S ribosomal protein L36
D1: 50S ribosomal protein L33
D3: 50S ribosomal protein L35
DV: 50S ribosomal protein L25
D2: 50S ribosomal protein L34
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DX: 50S ribosomal protein L29
DH: 50S ribosomal protein L9
DJ: 50S ribosomal protein L13
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DQ: 50S ribosomal protein L20
DS: 50S ribosomal protein L22
DU: 50S ribosomal protein L24
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DR: 50S ribosomal protein L21
DT: 50S ribosomal protein L23
DZ: 50S ribosomal protein L28
DW: 50S ribosomal protein L27
D6: ribosome recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,168,691227
Polymers2,164,42153
Non-polymers4,270174
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.900, 378.200, 736.300
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 , 3 types, 6 molecules AACABADABBDB

#1: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 83754040
#22: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357928
#23: RNA chain 23S rRNA


Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: GenBank: 33357927

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

#2: Protein 30S ribosomal protein S3


Mass: 25900.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V3
#3: Protein 30S ribosomal protein S4


Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V8
#4: Protein 30S ribosomal protein S5


Mass: 17498.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1
#5: Protein 30S ribosomal protein S6


Mass: 15727.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02358
#6: Protein 30S ribosomal protein S7


Mass: 19923.959 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02359
#7: Protein 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7W7
#8: Protein 30S ribosomal protein S9


Mass: 14755.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7X3
#9: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R5
#10: Protein 30S ribosomal protein S11


Mass: 13739.778 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R9
#11: Protein 30S ribosomal protein S12


Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3
#12: Protein 30S ribosomal protein S13


Mass: 12997.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7S9
#13: Protein 30S ribosomal protein S14


Mass: 11475.364 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG59
#14: Protein 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADZ4
#15: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T3
#16: Protein 30S ribosomal protein S17


Mass: 9593.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG63
#17: Protein 30S ribosomal protein S18


Mass: 8874.276 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7T7
#18: Protein 30S ribosomal protein S19


Mass: 10324.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U3
#19: Protein 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7U7
#20: Protein 30S ribosomal protein S2


Mass: 26650.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7V0
#21: Protein 30S ribosomal protein S21


Mass: 8392.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68679

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50S ribosomal protein ... , 29 types, 58 molecules BIDIBCDCBDDDBKDKBPDPBEDEBYDYB0D0B4D4B1D1B3D3BVDVB2D2BLDLBMDM...

#24: Protein 50S ribosomal protein L11


Mass: 14763.165 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7J7
#25: Protein 50S ribosomal protein L2


Mass: 29792.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60422
#26: Protein 50S ribosomal protein L3


Mass: 22277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60438
#27: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADY3
#28: Protein 50S ribosomal protein L19


Mass: 13028.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7K6
#29: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60723
#30: Protein 50S ribosomal protein L30


Mass: 6423.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG51
#31: Protein 50S ribosomal protein L32


Mass: 6332.249 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7N4
#32: Protein/peptide 50S ribosomal protein L36 / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q6
#33: Protein 50S ribosomal protein L33


Mass: 6257.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7N9
#34: Protein 50S ribosomal protein L35 / Ribosomal protein A


Mass: 7181.835 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#35: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P68919
#36: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7P5
#37: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P02413
#38: Protein 50S ribosomal protein L16


Mass: 15312.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADY7
#39: Protein 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M6
#40: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7R1
#41: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AA10
#42: Protein 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG44
#43: Protein 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#44: Protein 50S ribosomal protein L20


Mass: 13396.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L3
#45: Protein 50S ribosomal protein L22


Mass: 12253.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P61175
#46: Protein 50S ribosomal protein L24


Mass: 11208.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P60624
#47: Protein 50S ribosomal protein L5


Mass: 20202.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P62399
#48: Protein 50S ribosomal protein L6


Mass: 18801.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG55
#49: Protein 50S ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0AG48
#50: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0ADZ0
#51: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7M2
#52: Protein 50S ribosomal protein L27


Mass: 9015.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: P0A7L8

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Protein , 1 types, 2 molecules B6D6

#53: Protein ribosome recycling factor / Ribosome-releasing factor / RRF


Mass: 21029.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q9WX76

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Non-polymers , 3 types, 1972 molecules

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


Mass: 24.305 Da / Num. of mol.: 343 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#56: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1627 / 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: 14

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 277 K / Method: batch / pH: 7.5
Details: MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2PEG 800011
3MgCl211
4NH4Cl11
5spermine11
6spermidine11
7TRIS11
8EDTA11
9H2O11
10MPD12
11PEG 800012
12MgCl212
13NH4Cl12
14EDTA12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.111 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2006
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.111 Å / Relative weight: 1
ReflectionResolution: 3.3→123 Å / Num. obs: 738833 / % possible obs: 88 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.5
Reflection shellResolution: 3.3→3.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3 / % possible all: 52.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AVY, 2AW4, 2AW7, 2AWB

2avy
PDB Unreleased entry

2aw4
PDB Unreleased entry

2aw7
PDB Unreleased entry

2awb
PDB Unreleased entry


Resolution: 3.3→40 Å / Isotropic thermal model: grouped by residue / σ(F): 0 / Stereochemistry target values: torsional dynamics
RfactorNum. reflection% reflection
Rfree0.304 35383 -
Rwork0.275 --
all-860904 -
obs-738488 85.8 %
Displacement parametersBiso mean: 78.273 Å2
Refinement stepCycle: LAST / Resolution: 3.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18536 32831 60 300 51727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.928

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