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- PDB-6by1: E. coli pH03H9 complex -

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Basic information

Entry
Database: PDB / ID: 6by1
TitleE. coli pH03H9 complex
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Messenger RNA
  • Valine-specific transfer RNA
KeywordsRIBOSOME / mRNA / tRNA / helicase
Function / homology
Function and homology information


negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, 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 / negative regulation of translational initiation / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 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 L11, N-terminal / Ribosomal protein L17 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 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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 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 L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / :
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 ...: / : / : / : / 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 uL10 / 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 bL31 / 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 uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å
AuthorsAmiri, H. / Noller, H.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)17129 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)59140 United States
CitationJournal: Rna / Year: 2019
Title: Structural evidence for product stabilization by the ribosomal mRNA helicase.
Authors: Amiri, H. / Noller, H.F.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 12, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Oct 4, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S ribosomal RNA
CA: 23S ribosomal RNA
CB: 5S ribosomal RNA
AV: Valine-specific transfer RNA
AY: Valine-specific transfer RNA
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
C5: 50S ribosomal protein L10
CI: 50S ribosomal protein L11
CJ: 50S ribosomal protein L13
CK: 50S ribosomal protein L14
CL: 50S ribosomal protein L15
CM: 50S ribosomal protein L16
CN: 50S ribosomal protein L17
CO: 50S ribosomal protein L18
CP: 50S ribosomal protein L19
CQ: 50S ribosomal protein L20
CR: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
CW: 50S ribosomal protein L27
CX: 50S ribosomal protein L28
CY: 50S ribosomal protein L29
CZ: 50S ribosomal protein L30
C0: 50S ribosomal protein L31
C1: 50S ribosomal protein L32
C2: 50S ribosomal protein L33
C3: 50S ribosomal protein L34
C4: 50S ribosomal protein L35
C6: 50S ribosomal protein L36
AX: Messenger RNA
AW: Valine-specific transfer 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
BA: 16S ribosomal RNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
BV: Valine-specific transfer RNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L11
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L28
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D0: 50S ribosomal protein L31
D1: 50S ribosomal protein L32
D2: 50S ribosomal protein L33
D3: 50S ribosomal protein L34
D4: 50S ribosomal protein L35
D6: 50S ribosomal protein L36
BX: Messenger RNA
BW: Valine-specific transfer RNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,393,634561
Polymers4,382,556112
Non-polymers11,077449
Water70,5473916
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AA: 16S ribosomal RNA
CA: 23S ribosomal RNA
CB: 5S ribosomal RNA
AV: Valine-specific transfer RNA
AY: Valine-specific transfer RNA
CC: 50S ribosomal protein L2
CD: 50S ribosomal protein L3
CE: 50S ribosomal protein L4
CF: 50S ribosomal protein L5
CG: 50S ribosomal protein L6
CH: 50S ribosomal protein L9
C5: 50S ribosomal protein L10
CI: 50S ribosomal protein L11
CJ: 50S ribosomal protein L13
CK: 50S ribosomal protein L14
CL: 50S ribosomal protein L15
CM: 50S ribosomal protein L16
CN: 50S ribosomal protein L17
CO: 50S ribosomal protein L18
CP: 50S ribosomal protein L19
CQ: 50S ribosomal protein L20
CR: 50S ribosomal protein L21
CS: 50S ribosomal protein L22
CT: 50S ribosomal protein L23
CU: 50S ribosomal protein L24
CV: 50S ribosomal protein L25
CW: 50S ribosomal protein L27
CX: 50S ribosomal protein L28
CY: 50S ribosomal protein L29
CZ: 50S ribosomal protein L30
C0: 50S ribosomal protein L31
C1: 50S ribosomal protein L32
C2: 50S ribosomal protein L33
C3: 50S ribosomal protein L34
C4: 50S ribosomal protein L35
C6: 50S ribosomal protein L36
AX: Messenger RNA
AW: Valine-specific transfer 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,215,012284
Polymers2,209,41257
Non-polymers5,599227
Water1,00956
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BA: 16S ribosomal RNA
DA: 23S ribosomal RNA
DB: 5S ribosomal RNA
BV: Valine-specific transfer RNA
DC: 50S ribosomal protein L2
DD: 50S ribosomal protein L3
DE: 50S ribosomal protein L4
DF: 50S ribosomal protein L5
DG: 50S ribosomal protein L6
DH: 50S ribosomal protein L9
DI: 50S ribosomal protein L11
DJ: 50S ribosomal protein L13
DK: 50S ribosomal protein L14
DL: 50S ribosomal protein L15
DM: 50S ribosomal protein L16
DN: 50S ribosomal protein L17
DO: 50S ribosomal protein L18
DP: 50S ribosomal protein L19
DQ: 50S ribosomal protein L20
DR: 50S ribosomal protein L21
DS: 50S ribosomal protein L22
DT: 50S ribosomal protein L23
DU: 50S ribosomal protein L24
DV: 50S ribosomal protein L25
DW: 50S ribosomal protein L27
DX: 50S ribosomal protein L28
DY: 50S ribosomal protein L29
DZ: 50S ribosomal protein L30
D0: 50S ribosomal protein L31
D1: 50S ribosomal protein L32
D2: 50S ribosomal protein L33
D3: 50S ribosomal protein L34
D4: 50S ribosomal protein L35
D6: 50S ribosomal protein L36
BX: Messenger RNA
BW: Valine-specific transfer RNA
BB: 30S ribosomal protein S2
BC: 30S ribosomal protein S3
BD: 30S ribosomal protein S4
BE: 30S ribosomal protein S5
BF: 30S ribosomal protein S6
BG: 30S ribosomal protein S7
BH: 30S ribosomal protein S8
BI: 30S ribosomal protein S9
BJ: 30S ribosomal protein S10
BK: 30S ribosomal protein S11
BL: 30S ribosomal protein S12
BM: 30S ribosomal protein S13
BN: 30S ribosomal protein S14
BO: 30S ribosomal protein S15
BP: 30S ribosomal protein S16
BQ: 30S ribosomal protein S17
BR: 30S ribosomal protein S18
BS: 30S ribosomal protein S19
BT: 30S ribosomal protein S20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,178,622277
Polymers2,173,14455
Non-polymers5,478222
Water95553
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.656, 433.909, 623.532
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 , 5 types, 13 molecules AABACADACBDBAVAYAWBVBWAXBX

#1: RNA chain 16S ribosomal RNA /


Mass: 499360.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1126835768
#2: RNA chain 23S ribosomal RNA /


Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 687670942
#3: RNA chain 5S ribosomal RNA /


Mass: 38177.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1266940032
#4: RNA chain
Valine-specific transfer RNA


Mass: 24483.572 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1275521620
#36: RNA chain Messenger RNA /


Mass: 14995.027 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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50S ribosomal protein ... , 31 types, 61 molecules CCDCCDDDCEDECFDFCGDGCHDHC5CIDICJDJCKDKCLDLCMDMCNDNCODOCPDPCQ...

#5: Protein 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29663.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60422
#6: Protein 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60438
#7: Protein 50S ribosomal protein L4 / / Large ribosomal subunit protein uL4


Mass: 19998.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60723
#8: Protein 50S ribosomal protein L5 / / Large ribosomal subunit protein uL5


Mass: 20073.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P62399
#9: Protein 50S ribosomal protein L6 / / Large ribosomal subunit protein uL6


Mass: 18801.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG55
#10: Protein 50S ribosomal protein L9 / / Large ribosomal subunit protein bL9


Mass: 15789.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R1
#11: Protein 50S ribosomal protein L10 / / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 11784.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7J3
#12: Protein 50S ribosomal protein L11 / / Large ribosomal subunit protein uL11


Mass: 7450.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7J7
#13: Protein 50S ribosomal protein L13 / / Large ribosomal subunit protein uL13


Mass: 16050.606 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AA10
#14: Protein 50S ribosomal protein L14 / / Large ribosomal subunit protein uL14


Mass: 13451.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADY3
#15: Protein 50S ribosomal protein L15 / / Large ribosomal subunit protein uL15


Mass: 14877.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02413
#16: Protein 50S ribosomal protein L16 / / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADY7
#17: Protein 50S ribosomal protein L17 / / Large ribosomal subunit protein bL17


Mass: 13851.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG44
#18: Protein 50S ribosomal protein L18 / / Large ribosomal subunit protein uL18


Mass: 12663.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0C018
#19: Protein 50S ribosomal protein L19 / / Large ribosomal subunit protein bL19


Mass: 13028.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7K6
#20: Protein 50S ribosomal protein L20 / / Large ribosomal subunit protein bL20


Mass: 13396.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7L3
#21: Protein 50S ribosomal protein L21 / / Large ribosomal subunit protein bL21


Mass: 11586.374 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG48
#22: Protein 50S ribosomal protein L22 / / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P61175
#23: Protein 50S ribosomal protein L23 / / Large ribosomal subunit protein uL23


Mass: 10546.472 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADZ0
#24: Protein 50S ribosomal protein L24 /


Mass: 11078.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P60625, UniProt: P60624*PLUS
#25: Protein 50S ribosomal protein L25 / / Large ribosomal subunit protein bL25


Mass: 10713.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P68919
#26: Protein 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 8174.394 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7L8
#27: Protein 50S ribosomal protein L28 / / Large ribosomal subunit protein bL28


Mass: 8896.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M2
#28: Protein 50S ribosomal protein L29 / / Large ribosomal subunit protein uL29


Mass: 7286.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M6
#29: Protein 50S ribosomal protein L30 / / Large ribosomal subunit protein uL30


Mass: 6423.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG51
#30: Protein/peptide 50S ribosomal protein L31 / / Large ribosomal subunit protein bL31-A


Mass: 4262.888 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7M9
#31: Protein 50S ribosomal protein L32 / / Large ribosomal subunit protein bL32


Mass: 6332.249 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7N4
#32: Protein/peptide 50S ribosomal protein L33 / / Large ribosomal subunit protein bL33


Mass: 5814.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7N9
#33: Protein/peptide 50S ribosomal protein L34 / / Large ribosomal subunit protein bL34


Mass: 5397.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7P5
#34: Protein 50S ribosomal protein L35 / / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 6947.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7Q1
#35: Protein/peptide 50S ribosomal protein L36 / / Large ribosomal subunit protein bL36-A / Ribosomal protein B


Mass: 4377.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7Q6

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30S ribosomal protein ... , 19 types, 38 molecules ABBBACBCADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBLAMBMANBNAOBOAPBP...

#37: Protein 30S ribosomal protein S2 / / Small ribosomal subunit protein uS2


Mass: 25015.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V0
#38: Protein 30S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 23078.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V3
#39: Protein 30S ribosomal protein S4 / / Small ribosomal subunit protein uS4


Mass: 23383.002 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7V8
#40: Protein 30S ribosomal protein S5 / / Small ribosomal subunit protein uS5


Mass: 15804.282 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W1
#41: Protein 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 11669.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02358
#42: Protein 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02359
#43: Protein 30S ribosomal protein S8 / / Small ribosomal subunit protein uS8


Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7W7
#44: Protein 30S ribosomal protein S9 / / Small ribosomal subunit protein uS9


Mass: 14886.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7X3
#45: Protein 30S ribosomal protein S10 / / Small ribosomal subunit protein uS10


Mass: 11196.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R5
#46: Protein 30S ribosomal protein S11 / / Small ribosomal subunit protein uS11


Mass: 12487.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7R9
#47: Protein 30S ribosomal protein S12 / / Small ribosomal subunit protein uS12


Mass: 13636.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S3
#48: Protein 30S ribosomal protein S13 / / Small ribosomal subunit protein uS13


Mass: 12625.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7S9
#49: Protein 30S ribosomal protein S14 / / Small ribosomal subunit protein uS14


Mass: 11606.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG59
#50: Protein 30S ribosomal protein S15 / / Small ribosomal subunit protein uS15


Mass: 10290.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0ADZ4
#51: Protein 30S ribosomal protein S16 / / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T3
#52: Protein 30S ribosomal protein S17 / / Small ribosomal subunit protein uS17


Mass: 9263.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AG63
#53: Protein 30S ribosomal protein S18 / / Small ribosomal subunit protein bS18


Mass: 6466.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7T7
#54: Protein 30S ribosomal protein S19 / / Small ribosomal subunit protein uS19


Mass: 9057.626 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U3
#55: Protein 30S ribosomal protein S20 / / Small ribosomal subunit protein bS20


Mass: 9506.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0A7U7

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Non-polymers , 3 types, 4365 molecules

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


Mass: 24.305 Da / Num. of mol.: 445 / 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
#58: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3916 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 2000, PEP629, potassium thiocyanate, tris acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.94→59.994 Å / Num. obs: 501982 / % possible obs: 99.9 % / Redundancy: 8.172 % / Biso Wilson estimate: 137.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.571 / Rrim(I) all: 0.609 / Χ2: 0.904 / Net I/σ(I): 3.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.94-4.046.1412.4650.85360440.2752.69399.8
4.04-4.16.1392.3480.93199860.3022.56599.8
4.1-4.26.1472.1980.99308470.3162.40199.9
4.2-4.36.6362.2881.09280690.3452.4899.8
4.3-4.47.2632.4491.13255760.3512.63599.8
4.4-4.57.4482.2771.24233570.392.44599.9
4.5-4.67.6422.0881.36214150.4182.23999.9
4.6-58.2411.8811.56694530.4692.00899.9
5-69.3781.3352.281033690.6491.415100
6-89.330.7024.03825660.8750.743100
8-129.1190.22710.67428760.9870.24100
12-208.6320.0922.04144400.9960.09699.9
20-308.1160.04336.1929110.9990.04599.8
30-59.9947.0140.03937.9410730.9990.04281.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V9D

4v9d


Resolution: 3.94→59.994 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.44
RfactorNum. reflection% reflection
Rfree0.2692 10091 2.01 %
Rwork0.249 --
obs0.2494 501933 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 366.01 Å2 / Biso mean: 136.3538 Å2 / Biso min: 20.06 Å2
Refinement stepCycle: final / Resolution: 3.94→59.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms87682 203716 441 3937 295776
Biso mean--94.19 103.58 -
Num. residues----20717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004316972
X-RAY DIFFRACTIONf_angle_d0.954474956
X-RAY DIFFRACTIONf_chiral_restr0.04860842
X-RAY DIFFRACTIONf_plane_restr0.00624898
X-RAY DIFFRACTIONf_dihedral_angle_d17.181148328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.94-3.98480.3613510.34671628816639100
3.9848-4.03160.36663290.34191621116540100
4.0316-4.08080.34383070.33411630216609100
4.0808-4.13240.37933000.33591629916599100
4.1324-4.18680.34943400.33051622916569100
4.1868-4.24410.3473200.3231632216642100
4.2441-4.30480.34163180.31221631616634100
4.3048-4.3690.33873310.31751623716568100
4.369-4.43720.35943280.32011630016628100
4.4372-4.510.33193320.31081633016662100
4.51-4.58770.33083350.30871630016635100
4.5877-4.67110.32563390.29421627516614100
4.6711-4.76090.30453400.28941628716627100
4.7609-4.8580.30713250.2871634316668100
4.858-4.96360.31913300.28071637016700100
4.9636-5.0790.30063150.2711635116666100
5.079-5.2060.28193610.26021634016701100
5.206-5.34660.27323530.25851634916702100
5.3466-5.50390.2733230.25151639416717100
5.5039-5.68140.28813460.24951638516731100
5.6814-5.88430.27413340.24671642716761100
5.8843-6.11970.27773700.24481634616716100
6.1197-6.39790.2673220.24841645216774100
6.3979-6.73480.2693260.23691643716763100
6.7348-7.15610.25553350.22611648416819100
7.1561-7.70760.23963380.21691649516833100
7.7076-8.48130.22653760.21831657516951100
8.4813-9.70410.23593650.21331657316938100
9.7041-12.20920.20163250.18661674717072100
12.2092-60.00110.1823770.175170781745599

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