[English] 日本語
Yorodumi
- PDB-4v5b: Structure of PDF binding helix in complex with the ribosome. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v5b
TitleStructure of PDF binding helix in complex with the ribosome.
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • 16S RIBOSOMAL RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • C-TERM HELIX PDF
KeywordsRIBOSOME / TRANSLATION / PEPTIDE DEFORMYLASE / RNA-PROTEIN COMPLEX / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / 50S RIBOSOMAL SUBUNIT / ANTIBIOTIC RESISTANCE / NASCENT CHAIN PROCESSING / RNA-BINDING / TRANSLATION REGULATION / TRNA BINDING / PROTEIN BIOSYNTHESIS
Function / homology
Function and homology information


co-translational protein modification / peptide deformylase / peptide deformylase 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 ...co-translational protein modification / peptide deformylase / peptide deformylase 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 / translation repressor activity / negative regulation of translational initiation / 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 / transcription elongation factor complex / positive regulation of RNA splicing / DNA endonuclease activity / : / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / ferrous iron binding / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / endonuclease activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / hydrolase activity / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / 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 L31 type A / Ribosomal protein S21 superfamily ...Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / 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 L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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 S14/S29 / 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 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 L27, conserved site / Ribosomal protein S6, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6 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 L14P, bacterial-type / Ribosomal protein S4, 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 protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / 30S ribosomal protein S11 / 30S ribosomal protein S8 / 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 uS4 / 30S ribosomal protein S11 / 30S ribosomal protein S8 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / 30S ribosomal protein S6 / 30S ribosomal protein S6 / Peptide deformylase / Large ribosomal subunit protein uL11 / 50S ribosomal protein L11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / 50S ribosomal protein L27 / Large ribosomal subunit protein uL29 / 50S ribosomal protein L29 / Large ribosomal subunit protein bL31 / 50S ribosomal protein L31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / 50S ribosomal protein L34 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL36A / 50S ribosomal protein L36 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS16 / 30S ribosomal protein S16 / Small ribosomal subunit protein bS18 / 30S ribosomal protein S18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / 30S ribosomal protein S20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / 30S ribosomal protein S3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / 30S ribosomal protein S9 / 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 / 50S ribosomal protein L6 / Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / 50S ribosomal protein L2 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / 50S ribosomal protein L4 / Large ribosomal subunit protein uL22 / 50S ribosomal protein L22 / Large ribosomal subunit protein uL5 / 50S ribosomal protein L5 / 30S ribosomal protein S7 / Small ribosomal subunit protein bS21 / 30S ribosomal protein S21 / Large ribosomal subunit protein bL25 / 30S ribosomal protein S19 / 50S ribosomal protein L30 / 30S ribosomal protein S4 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L32 / 30S ribosomal protein S20 / 50S ribosomal protein L23 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsBingel-Erlenmeyer, R. / Kohler, R. / Kramer, G. / Sandikci, A. / Antolic, S. / Maier, T. / Schaffitzel, C. / Wiedmann, B. / Bukau, B. / Ban, N.
CitationJournal: Nature / Year: 2008
Title: A Peptide Deformylase-Ribosome Complex Reveals Mechanism of Nascent Chain Processing.
Authors: Bingel-Erlenmeyer, R. / Kohler, R. / Kramer, G. / Sandikci, A. / Antolic, S. / Maier, T. / Schaffitzel, C. / Wiedmann, B. / Bukau, B. / Ban, N.
History
DepositionNov 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 2VHM, 2VHN, 2VHO, 2VHP
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Mar 14, 2018Group: Database references / Structure summary / Category: citation / entity
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _entity.src_method
Revision 1.3Apr 20, 2022Group: Database references / Derived calculations / Category: database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.ptnr2_label_seq_id
Revision 1.4Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.5Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A0: 50S RIBOSOMAL PROTEIN L32
A1: 50S RIBOSOMAL PROTEIN L33
A2: 50S RIBOSOMAL PROTEIN L34
A3: 50S RIBOSOMAL PROTEIN L35
A4: 50S RIBOSOMAL PROTEIN L36
A5: C-TERM HELIX PDF
AA: 5S RIBOSOMAL RNA
AB: 23S RIBOSOMAL RNA
AC: 50S RIBOSOMAL PROTEIN L2
AD: 50S RIBOSOMAL PROTEIN L3
AE: 50S RIBOSOMAL PROTEIN L4
AF: 50S RIBOSOMAL PROTEIN L5
AG: 50S RIBOSOMAL PROTEIN L6
AH: 50S RIBOSOMAL PROTEIN L9
AI: 50S RIBOSOMAL PROTEIN L11
AJ: 50S RIBOSOMAL PROTEIN L13
AK: 50S RIBOSOMAL PROTEIN L14
AL: 50S RIBOSOMAL PROTEIN L15
AM: 50S RIBOSOMAL PROTEIN L16
AN: 50S RIBOSOMAL PROTEIN L17
AO: 50S RIBOSOMAL PROTEIN L18
AP: 50S RIBOSOMAL PROTEIN L19
AQ: 50S RIBOSOMAL PROTEIN L20
AR: 50S RIBOSOMAL PROTEIN L21
AS: 50S RIBOSOMAL PROTEIN L22
AT: 50S RIBOSOMAL PROTEIN L23
AU: 50S RIBOSOMAL PROTEIN L24
AV: 50S RIBOSOMAL PROTEIN L25
AW: 50S RIBOSOMAL PROTEIN L27
AX: 50S RIBOSOMAL PROTEIN L29
AY: 50S RIBOSOMAL PROTEIN L30
AZ: 50S RIBOSOMAL PROTEIN L31
BA: 16S RIBOSOMAL 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
BU: 30S RIBOSOMAL PROTEIN S21
C0: 50S RIBOSOMAL PROTEIN L32
C1: 50S RIBOSOMAL PROTEIN L33
C2: 50S RIBOSOMAL PROTEIN L34
C3: 50S RIBOSOMAL PROTEIN L35
C4: 50S RIBOSOMAL PROTEIN L36
CA: 5S RIBOSOMAL RNA
CB: 23S RIBOSOMAL 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
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 L29
CY: 50S RIBOSOMAL PROTEIN L30
CZ: 50S RIBOSOMAL PROTEIN L31
DA: 16S RIBOSOMAL RNA
DB: 30S RIBOSOMAL PROTEIN S2
DC: 30S RIBOSOMAL PROTEIN S3
DD: 30S RIBOSOMAL PROTEIN S4
DE: 30S RIBOSOMAL PROTEIN S5
DF: 30S RIBOSOMAL PROTEIN S6
DG: 30S RIBOSOMAL PROTEIN S7
DH: 30S RIBOSOMAL PROTEIN S8
DI: 30S RIBOSOMAL PROTEIN S9
DJ: 30S RIBOSOMAL PROTEIN S10
DK: 30S RIBOSOMAL PROTEIN S11
DL: 30S RIBOSOMAL PROTEIN S12
DM: 30S RIBOSOMAL PROTEIN S13
DN: 30S RIBOSOMAL PROTEIN S14
DO: 30S RIBOSOMAL PROTEIN S15
DP: 30S RIBOSOMAL PROTEIN S16
DQ: 30S RIBOSOMAL PROTEIN S17
DR: 30S RIBOSOMAL PROTEIN S18
DS: 30S RIBOSOMAL PROTEIN S19
DT: 30S RIBOSOMAL PROTEIN S20
DU: 30S RIBOSOMAL PROTEIN S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,295,349448
Polymers4,287,012105
Non-polymers8,337343
Water29,1301617
1
A0: 50S RIBOSOMAL PROTEIN L32
A1: 50S RIBOSOMAL PROTEIN L33
A2: 50S RIBOSOMAL PROTEIN L34
A3: 50S RIBOSOMAL PROTEIN L35
A4: 50S RIBOSOMAL PROTEIN L36
A5: C-TERM HELIX PDF
AA: 5S RIBOSOMAL RNA
AB: 23S RIBOSOMAL RNA
AC: 50S RIBOSOMAL PROTEIN L2
AD: 50S RIBOSOMAL PROTEIN L3
AE: 50S RIBOSOMAL PROTEIN L4
AF: 50S RIBOSOMAL PROTEIN L5
AG: 50S RIBOSOMAL PROTEIN L6
AH: 50S RIBOSOMAL PROTEIN L9
AI: 50S RIBOSOMAL PROTEIN L11
AJ: 50S RIBOSOMAL PROTEIN L13
AK: 50S RIBOSOMAL PROTEIN L14
AL: 50S RIBOSOMAL PROTEIN L15
AM: 50S RIBOSOMAL PROTEIN L16
AN: 50S RIBOSOMAL PROTEIN L17
AO: 50S RIBOSOMAL PROTEIN L18
AP: 50S RIBOSOMAL PROTEIN L19
AQ: 50S RIBOSOMAL PROTEIN L20
AR: 50S RIBOSOMAL PROTEIN L21
AS: 50S RIBOSOMAL PROTEIN L22
AT: 50S RIBOSOMAL PROTEIN L23
AU: 50S RIBOSOMAL PROTEIN L24
AV: 50S RIBOSOMAL PROTEIN L25
AW: 50S RIBOSOMAL PROTEIN L27
AX: 50S RIBOSOMAL PROTEIN L29
AY: 50S RIBOSOMAL PROTEIN L30
AZ: 50S RIBOSOMAL PROTEIN L31
BA: 16S RIBOSOMAL 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
BU: 30S RIBOSOMAL PROTEIN S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,148,602223
Polymers2,144,47053
Non-polymers4,132170
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C0: 50S RIBOSOMAL PROTEIN L32
C1: 50S RIBOSOMAL PROTEIN L33
C2: 50S RIBOSOMAL PROTEIN L34
C3: 50S RIBOSOMAL PROTEIN L35
C4: 50S RIBOSOMAL PROTEIN L36
CA: 5S RIBOSOMAL RNA
CB: 23S RIBOSOMAL 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
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 L29
CY: 50S RIBOSOMAL PROTEIN L30
CZ: 50S RIBOSOMAL PROTEIN L31
DA: 16S RIBOSOMAL RNA
DB: 30S RIBOSOMAL PROTEIN S2
DC: 30S RIBOSOMAL PROTEIN S3
DD: 30S RIBOSOMAL PROTEIN S4
DE: 30S RIBOSOMAL PROTEIN S5
DF: 30S RIBOSOMAL PROTEIN S6
DG: 30S RIBOSOMAL PROTEIN S7
DH: 30S RIBOSOMAL PROTEIN S8
DI: 30S RIBOSOMAL PROTEIN S9
DJ: 30S RIBOSOMAL PROTEIN S10
DK: 30S RIBOSOMAL PROTEIN S11
DL: 30S RIBOSOMAL PROTEIN S12
DM: 30S RIBOSOMAL PROTEIN S13
DN: 30S RIBOSOMAL PROTEIN S14
DO: 30S RIBOSOMAL PROTEIN S15
DP: 30S RIBOSOMAL PROTEIN S16
DQ: 30S RIBOSOMAL PROTEIN S17
DR: 30S RIBOSOMAL PROTEIN S18
DS: 30S RIBOSOMAL PROTEIN S19
DT: 30S RIBOSOMAL PROTEIN S20
DU: 30S RIBOSOMAL PROTEIN S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,146,747225
Polymers2,142,54352
Non-polymers4,205173
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)208.181, 380.083, 736.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

+
50S RIBOSOMAL PROTEIN ... , 29 types, 58 molecules A0C0A1C1A2C2A3C3A4C4ACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCL...

#1: 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: Q0TIY5, UniProt: P0A7N4*PLUS
#2: Protein 50S RIBOSOMAL PROTEIN L33 /


Mass: 6257.436 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-55 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7N9
#3: 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: P0A7P6, UniProt: P0A7P5*PLUS
#4: Protein 50S RIBOSOMAL PROTEIN L35 /


Mass: 7181.835 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-65 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7Q1
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36 /


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: P0A7Q7, UniProt: P0A7Q6*PLUS
#9: Protein 50S RIBOSOMAL PROTEIN L2 /


Mass: 29923.619 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P60424, UniProt: P60422*PLUS
#10: 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: P60439, UniProt: P60438*PLUS
#11: 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: P60725, UniProt: P60723*PLUS
#12: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 20202.416 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-179 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P62401, UniProt: P62399*PLUS
#13: Protein 50S RIBOSOMAL PROTEIN L6 /


Mass: 18801.598 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-177 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0AG57, UniProt: P0AG55*PLUS
#14: 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
#15: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 14763.165 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-142 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7J8, UniProt: P0A7J7*PLUS
#16: 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: Q1R6A9, UniProt: P0AA10*PLUS
#17: 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: Q1R617, UniProt: P0ADY3*PLUS
#18: 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
#19: 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
#20: 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: Q0TCG7, UniProt: P0AG44*PLUS
#21: Protein 50S RIBOSOMAL PROTEIN L18 /


Mass: 12794.668 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-57 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0C018
#22: Protein 50S RIBOSOMAL PROTEIN L19 /


Mass: 13028.082 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-115 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7K6
#23: Protein 50S RIBOSOMAL PROTEIN L20 /


Mass: 13396.828 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-118 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7L3
#24: 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: Q0TCS4, UniProt: P0AG48*PLUS
#25: 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: P61176, UniProt: P61175*PLUS
#26: 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: Q1R606, UniProt: P0ADZ0*PLUS
#27: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 11208.054 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-104 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P60625, UniProt: P60624*PLUS
#28: 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
#29: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9015.344 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-85 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7L9, UniProt: P0A7L8*PLUS
#30: 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: P0A7M7, UniProt: P0A7M6*PLUS
#31: Protein 50S RIBOSOMAL PROTEIN L30 /


Mass: 6423.625 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-59 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TCF9, UniProt: P0AG51*PLUS
#32: Protein 50S RIBOSOMAL PROTEIN L31 /


Mass: 7887.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7N0, UniProt: P0A7M9*PLUS

-
Protein/peptide , 1 types, 1 molecules A5

#6: Protein/peptide C-TERM HELIX PDF


Mass: 1927.317 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6K3

-
RNA chain , 3 types, 6 molecules AACAABCBBADA

#7: RNA chain 5S RIBOSOMAL RNA /


Mass: 38790.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
#8: RNA chain 23S RIBOSOMAL RNA /


Mass: 941612.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
#33: RNA chain 16S RIBOSOMAL RNA /


Mass: 499690.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600

-
30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules BBDBBCDCBDDDBEDEBFDFBGDGBHDHBIDIBJDJBKDKBLDLBMDMBNDNBODOBPDP...

#34: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 26650.475 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-241 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7V1, UniProt: P0A7V0
#35: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 25900.117 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-233 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7V4, UniProt: P0A7V3
#36: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 23383.002 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-206 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: Q0TCG5, UniProt: A1AGI7, UniProt: P0A7V8*PLUS
#37: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 17498.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-167 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7W1, UniProt: P0A7W3
#38: 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: P0A4D0, UniProt: P0A4D1, UniProt: P02358*PLUS
#39: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 19923.959 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-156 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P66606, UniProt: P02359*PLUS
#40: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 14015.361 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: A1AGJ5, UniProt: P0A7W7
#41: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14755.074 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-130 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7X3, UniProt: P0A7X4
#42: 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, UniProt: P0A7R6
#43: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 13739.778 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-129 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: A1AGI8, UniProt: P0A7R9*PLUS
#44: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 13636.961 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-124 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7S3, UniProt: P0A7S4
#45: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 12997.271 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-118 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7T1, UniProt: P0A7S9
#46: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 11475.364 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-101 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0AG59, UniProt: P0AG61
#47: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10319.882 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q8X9M2, UniProt: P0ADZ4*PLUS
#48: 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, UniProt: P0A7T4
#49: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 9593.296 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-84 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: Q1R616, UniProt: P0AG65, UniProt: P0AG63*PLUS
#50: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 8874.276 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-75 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P0A7T7, UniProt: P0A7T9
#51: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10324.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-92 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: Q0TCE5, UniProt: P0A7U3*PLUS
#52: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 9577.268 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-87 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600
References: UniProt: Q0TLW7, UniProt: P0A7U9, UniProt: P0A7U7*PLUS
#53: Protein 30S RIBOSOMAL PROTEIN S21 /


Mass: 8524.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / References: UniProt: P68680, UniProt: P68679

-
Non-polymers , 2 types, 1960 molecules

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


Mass: 24.305 Da / Num. of mol.: 343 / Source method: obtained synthetically / Formula: Mg
#55: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1617 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A5, LEU 147 TO ALA

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.82 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.74→50 Å / Num. obs: 546832 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.1

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AW4

2aw4
PDB Unreleased entry


Resolution: 3.74→50 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.323 5544 1 %
Rwork0.259 --
obs-546832 91.5 %
Refinement stepCycle: LAST / Resolution: 3.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26327 63502 110 503 90442

+
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