[English] 日本語
Yorodumi
- PDB-4wf1: Crystal structure of the E. coli ribosome bound to negamycin. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wf1
TitleCrystal structure of the E. coli ribosome bound to negamycin.
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
KeywordsRibosome/Antibiotic / Protein biosynthesis / ribosomes / RNA / transfer / exit / peptidyl / 30S / 70S / 16S / ribosomal subunit / antibiotic / streptogramin / Ribosome-Antibiotic 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 / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity ...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 / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / translational termination / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / regulation of mRNA stability / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / response to reactive oxygen species / ribosome assembly / transcription elongation factor complex / DNA endonuclease activity / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / large ribosomal subunit / ribosome biogenesis / ribosome binding / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site ...Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / 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 L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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, 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/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33
Similarity search - Domain/homology
NEGAMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 ...NEGAMYCIN / : / : / 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 / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
Escherichia coli (E. coli)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.09 Å
AuthorsOlivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. ...Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. / Miller, M.D. / Prince, D.B. / Cate, J.H.D. / Buurman, E.T. / Blanchard, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.
Authors: Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. / Miller, M.D. / Prince, D.B. / Cate, J.H. / Buurman, ...Authors: Olivier, N.B. / Altman, R.B. / Noeske, J. / Basarab, G.S. / Code, E. / Ferguson, A.D. / Gao, N. / Huang, J. / Juette, M.F. / Livchak, S. / Miller, M.D. / Prince, D.B. / Cate, J.H. / Buurman, E.T. / Blanchard, S.C.
History
DepositionSep 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
SupersessionDec 10, 2014ID: 4WAO, 4WAP, 4WAQ, 4WAR
Revision 1.3Dec 10, 2014Group: Other
Revision 1.4Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist
Revision 1.5Dec 27, 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_struct_conn_angle / refine_hist / 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 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: 16S rRNA
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 S21
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
B5: 50S ribosomal protein L1
CA: 16S rRNA
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 S21
DA: 23S rRNA
DB: 5S rRNA
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 L32
D1: 50S ribosomal protein L33
D2: 50S ribosomal protein L34
D3: 50S ribosomal protein L35
D4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,265,690607
Polymers4,253,183105
Non-polymers12,507502
Water30,9681719
1
AA: 16S rRNA
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 S21
BA: 23S rRNA
BB: 5S rRNA
BC: 50S ribosomal protein L2
BD: 50S ribosomal protein L3
BE: 50S ribosomal protein L4
BF: 50S ribosomal protein L5
BG: 50S ribosomal protein L6
BH: 50S ribosomal protein L9
BI: 50S ribosomal protein L11
BJ: 50S ribosomal protein L13
BK: 50S ribosomal protein L14
BL: 50S ribosomal protein L15
BM: 50S ribosomal protein L16
BN: 50S ribosomal protein L17
BO: 50S ribosomal protein L18
BP: 50S ribosomal protein L19
BQ: 50S ribosomal protein L20
BR: 50S ribosomal protein L21
BS: 50S ribosomal protein L22
BT: 50S ribosomal protein L23
BU: 50S ribosomal protein L24
BV: 50S ribosomal protein L25
BW: 50S ribosomal protein L27
BX: 50S ribosomal protein L28
BY: 50S ribosomal protein L29
BZ: 50S ribosomal protein L30
B0: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
B5: 50S ribosomal protein L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,144,391325
Polymers2,137,73953
Non-polymers6,652272
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
CA: 16S rRNA
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 S21
DA: 23S rRNA
DB: 5S rRNA
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 L32
D1: 50S ribosomal protein L33
D2: 50S ribosomal protein L34
D3: 50S ribosomal protein L35
D4: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,121,299282
Polymers2,115,44352
Non-polymers5,855230
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.910, 434.310, 624.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
RNA chain , 3 types, 6 molecules AACABADABBDB

#1: RNA chain 16S rRNA


Mass: 498725.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: GenBank: 545778205
#22: RNA chain 23S rRNA


Mass: 941306.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: GenBank: 409785
#23: RNA chain 5S rRNA


Mass: 38483.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K-12 substr. MG1655 (bacteria)
References: GenBank: 545778205

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

#2: Protein 30S ribosomal protein S2


Mass: 24253.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V0
#3: Protein 30S ribosomal protein S3


Mass: 23078.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7V3
#4: 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: K12 / References: UniProt: P0A7V8
#5: Protein 30S ribosomal protein S5


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


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


Mass: 16861.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02359
#8: 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: K12 / References: UniProt: P0A7W7
#9: Protein 30S ribosomal protein S9


Mass: 14554.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10


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


Mass: 12487.200 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7R9
#12: 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: K12 / References: UniProt: P0A7S3
#13: Protein 30S ribosomal protein S13


Mass: 12625.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7S9
#14: 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: K12 / References: UniProt: P0AG59
#15: Protein 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0ADZ4
#16: 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: K12 / References: UniProt: P0A7T3
#17: Protein 30S ribosomal protein S17


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


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


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


Mass: 9506.190 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21


Mass: 6067.081 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P68679

+
50S ribosomal protein ... , 30 types, 59 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDPBQDQ...

#24: Protein 50S ribosomal protein L2


Mass: 29663.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P60422
#25: 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: K12 / References: UniProt: P60438
#26: 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: K12 / References: UniProt: P60723
#27: Protein 50S ribosomal protein L5


Mass: 20073.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P62399
#28: 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: K12 / References: UniProt: P0AG55
#29: 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: K12 / References: UniProt: P0A7R1
#30: 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: K12 / References: UniProt: P0A7J7
#31: 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: K12 / References: UniProt: P0AA10
#32: Protein 50S ribosomal protein L14


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


Mass: 14877.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P02413
#34: 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: K12 / References: UniProt: P0ADY7
#35: Protein 50S ribosomal protein L17


Mass: 13721.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0AG44
#36: Protein 50S ribosomal protein L18


Mass: 12663.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0C018
#37: 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: K12 / References: UniProt: P0A7K6
#38: 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: K12 / References: UniProt: P0A7L3
#39: 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: K12 / References: UniProt: P0AG48
#40: 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: K12 / References: UniProt: P61175
#41: Protein 50S ribosomal protein L23


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


Mass: 11078.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P60624
#43: 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: K12 / References: UniProt: P68919
#44: Protein 50S ribosomal protein L27


Mass: 8275.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7L8
#45: Protein 50S ribosomal protein L28


Mass: 8896.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7M2
#46: 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: K12 / References: UniProt: P0A7M6
#47: 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: K12 / References: UniProt: P0AG51
#48: 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: K12 / References: UniProt: P0A7N4
#49: Protein/peptide 50S ribosomal protein L33


Mass: 5814.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7N9
#50: 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: K12 / References: UniProt: P0A7P5
#51: 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: K12 / References: UniProt: P0A7Q1
#52: 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: K12 / References: UniProt: P0A7Q6
#53: Protein 50S ribosomal protein L1


Mass: 22295.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP7

-
Non-polymers , 4 types, 2221 molecules

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


Mass: 24.305 Da / Num. of mol.: 499 / 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: Chemical ChemComp-NEG / NEGAMYCIN / 3,6-DIAMINO-1-[2-(CARBOXYMETHYL)-2-METHYLHYDRAZINO]-2,3,4,6-TETRADEOXY-L-THREO-HEXOSE


Mass: 248.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20N4O4
#57: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1719 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5 / Details: PEG8k, MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→41.14 Å / Num. obs: 1043787 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 72.66 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.058 / Net I/σ(I): 14.9 / Num. measured all: 6209734 / Scaling rejects: 444
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.09-3.2760.8042.610084251681000.7490.358100
9.26-41.145.60.02861.3222208395860.9940.01398.7

-
Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.09→41.136 Å / FOM work R set: 0.841 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 4190 0.4 %
Rwork0.2018 1034861 -
obs0.2019 1039051 99.94 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.16 Å2 / Biso mean: 67.48 Å2 / Biso min: 1.05 Å2
Refinement stepCycle: final / Resolution: 3.09→41.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90489 195478 72 203 286242
Biso mean--52.42 49.59 -
Num. residues----3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008312342
X-RAY DIFFRACTIONf_angle_d1.252467929
X-RAY DIFFRACTIONf_chiral_restr0.05359358
X-RAY DIFFRACTIONf_plane_restr0.00625043
X-RAY DIFFRACTIONf_dihedral_angle_d16.354144818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.09-3.20040.2744210.2498102829103250
3.2004-3.32850.27083680.2266102876103244
3.3285-3.47990.23954120.2121103061103473
3.4799-3.66330.24784230.2004103101103524
3.6633-3.89260.24953810.1932103112103493
3.8926-4.19290.24394150.1949103286103701
4.1929-4.61430.24434400.1952103488103928
4.6143-5.28080.23364360.1897103630104066
5.2808-6.64880.24334480.1923104045104493
6.6488-41.13940.23874460.2062105433105879

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more