[English] 日本語
Yorodumi
- PDB-4v97: Crystal structure of the bacterial ribosome ram mutation G299A. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v97
TitleCrystal structure of the bacterial ribosome ram mutation G299A.
Components
  • (30S ribosomal protein ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 30
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • E-SITE TRNA PHE OR A-SITE tRNA Phe
  • P-SITE tRNA fMet
  • mRNA
KeywordsRIBOSOME / Protein biosynthesis / ribosomes / RNA / tRNA / transfer / ribosomal ambiguity mutation / ram / 30S / 70S / 16S / ribosomal subunit
Function / homology
Function and homology information


regulation of translation / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit ...regulation of translation / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
30S ribosomal protein Thx / 30S ribosomal protein Thx / Ribosomal protein L1, bacterial-type / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z ...30S ribosomal protein Thx / 30S ribosomal protein Thx / Ribosomal protein L1, bacterial-type / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein 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 L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / 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 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36 / Ribosomal protein S11, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal protein S18, conserved site / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18 signature. / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / : / L28p-like / Ribosomal protein S15, bacterial-type
Similarity search - Domain/homology
PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...PAROMOMYCIN / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.516 Å
AuthorsFagan, C.E. / Dunkle, J.A. / Maehigashi, T. / Dunham, C.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
Authors: Fagan, C.E. / Dunkle, J.A. / Maehigashi, T. / Dang, M.N. / Devaraj, A. / Miles, S.J. / Qin, D. / Fredrick, K. / Dunham, C.M.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4EJ9, 4EJA, 4EJB, 4EJC
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 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 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AV: P-SITE tRNA fMet
AW: E-SITE TRNA PHE OR A-SITE tRNA Phe
AX: mRNA
AY: E-SITE TRNA PHE OR A-SITE tRNA Phe
BA: 23S rRNA
BB: 5S rRNA
BC: 50S RIBOSOMAL PROTEIN L1
BD: 50S RIBOSOMAL PROTEIN L2
BE: 50S RIBOSOMAL PROTEIN L3
BF: 50S RIBOSOMAL PROTEIN L4
BG: 50S RIBOSOMAL PROTEIN L5
BH: 50S RIBOSOMAL PROTEIN L6
BI: 50S RIBOSOMAL PROTEIN L9
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
B4: 50S RIBOSOMAL PROTEIN L31
B5: 50S RIBOSOMAL PROTEIN L32
B6: 50S RIBOSOMAL PROTEIN L33
B7: 50S RIBOSOMAL PROTEIN L34
B8: 50S RIBOSOMAL PROTEIN L35
B9: 50S RIBOSOMAL PROTEIN L36
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 type Z
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein Thx
CV: P-SITE tRNA fMet
CW: E-SITE TRNA PHE OR A-SITE tRNA Phe
CX: mRNA
CY: E-SITE TRNA PHE OR A-SITE tRNA Phe
DA: 23S rRNA
DB: 5S rRNA
DC: 50S RIBOSOMAL PROTEIN L1
DD: 50S RIBOSOMAL PROTEIN L2
DE: 50S RIBOSOMAL PROTEIN L3
DF: 50S RIBOSOMAL PROTEIN L4
DG: 50S RIBOSOMAL PROTEIN L5
DH: 50S RIBOSOMAL PROTEIN L6
DI: 50S RIBOSOMAL PROTEIN L9
DN: 50S RIBOSOMAL PROTEIN L13
DO: 50S RIBOSOMAL PROTEIN L14
DP: 50S RIBOSOMAL PROTEIN L15
DQ: 50S RIBOSOMAL PROTEIN L16
DR: 50S RIBOSOMAL PROTEIN L17
DS: 50S RIBOSOMAL PROTEIN L18
DT: 50S RIBOSOMAL PROTEIN L19
DU: 50S RIBOSOMAL PROTEIN L20
DV: 50S RIBOSOMAL PROTEIN L21
DW: 50S RIBOSOMAL PROTEIN L22
DX: 50S RIBOSOMAL PROTEIN L23
DY: 50S RIBOSOMAL PROTEIN L24
DZ: 50S RIBOSOMAL PROTEIN L25
D0: 50S RIBOSOMAL PROTEIN L27
D1: 50S RIBOSOMAL PROTEIN L28
D2: 50S RIBOSOMAL PROTEIN L29
D3: 50S RIBOSOMAL PROTEIN L30
D4: 50S RIBOSOMAL PROTEIN L31
D5: 50S RIBOSOMAL PROTEIN L32
D6: 50S RIBOSOMAL PROTEIN L33
D7: 50S RIBOSOMAL PROTEIN L34
D8: 50S RIBOSOMAL PROTEIN L35
D9: 50S RIBOSOMAL PROTEIN L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,576,9331153
Polymers4,550,333114
Non-polymers26,6001039
Water00
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 type Z
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
AU: 30S ribosomal protein Thx
AV: P-SITE tRNA fMet
AW: E-SITE TRNA PHE OR A-SITE tRNA Phe
AX: mRNA
AY: E-SITE TRNA PHE OR A-SITE tRNA Phe
BA: 23S rRNA
BB: 5S rRNA
BC: 50S RIBOSOMAL PROTEIN L1
BD: 50S RIBOSOMAL PROTEIN L2
BE: 50S RIBOSOMAL PROTEIN L3
BF: 50S RIBOSOMAL PROTEIN L4
BG: 50S RIBOSOMAL PROTEIN L5
BH: 50S RIBOSOMAL PROTEIN L6
BI: 50S RIBOSOMAL PROTEIN L9
BN: 50S RIBOSOMAL PROTEIN L13
BO: 50S RIBOSOMAL PROTEIN L14
BP: 50S RIBOSOMAL PROTEIN L15
BQ: 50S RIBOSOMAL PROTEIN L16
BR: 50S RIBOSOMAL PROTEIN L17
BS: 50S RIBOSOMAL PROTEIN L18
BT: 50S RIBOSOMAL PROTEIN L19
BU: 50S RIBOSOMAL PROTEIN L20
BV: 50S RIBOSOMAL PROTEIN L21
BW: 50S RIBOSOMAL PROTEIN L22
BX: 50S RIBOSOMAL PROTEIN L23
BY: 50S RIBOSOMAL PROTEIN L24
BZ: 50S RIBOSOMAL PROTEIN L25
B0: 50S RIBOSOMAL PROTEIN L27
B1: 50S RIBOSOMAL PROTEIN L28
B2: 50S RIBOSOMAL PROTEIN L29
B3: 50S RIBOSOMAL PROTEIN L30
B4: 50S RIBOSOMAL PROTEIN L31
B5: 50S RIBOSOMAL PROTEIN L32
B6: 50S RIBOSOMAL PROTEIN L33
B7: 50S RIBOSOMAL PROTEIN L34
B8: 50S RIBOSOMAL PROTEIN L35
B9: 50S RIBOSOMAL PROTEIN L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,287,020517
Polymers2,275,16657
Non-polymers11,854460
Water0
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 type Z
CO: 30S ribosomal protein S15
CP: 30S ribosomal protein S16
CQ: 30S ribosomal protein S17
CR: 30S ribosomal protein S18
CS: 30S ribosomal protein S19
CT: 30S ribosomal protein S20
CU: 30S ribosomal protein Thx
CV: P-SITE tRNA fMet
CW: E-SITE TRNA PHE OR A-SITE tRNA Phe
CX: mRNA
CY: E-SITE TRNA PHE OR A-SITE tRNA Phe
DA: 23S rRNA
DB: 5S rRNA
DC: 50S RIBOSOMAL PROTEIN L1
DD: 50S RIBOSOMAL PROTEIN L2
DE: 50S RIBOSOMAL PROTEIN L3
DF: 50S RIBOSOMAL PROTEIN L4
DG: 50S RIBOSOMAL PROTEIN L5
DH: 50S RIBOSOMAL PROTEIN L6
DI: 50S RIBOSOMAL PROTEIN L9
DN: 50S RIBOSOMAL PROTEIN L13
DO: 50S RIBOSOMAL PROTEIN L14
DP: 50S RIBOSOMAL PROTEIN L15
DQ: 50S RIBOSOMAL PROTEIN L16
DR: 50S RIBOSOMAL PROTEIN L17
DS: 50S RIBOSOMAL PROTEIN L18
DT: 50S RIBOSOMAL PROTEIN L19
DU: 50S RIBOSOMAL PROTEIN L20
DV: 50S RIBOSOMAL PROTEIN L21
DW: 50S RIBOSOMAL PROTEIN L22
DX: 50S RIBOSOMAL PROTEIN L23
DY: 50S RIBOSOMAL PROTEIN L24
DZ: 50S RIBOSOMAL PROTEIN L25
D0: 50S RIBOSOMAL PROTEIN L27
D1: 50S RIBOSOMAL PROTEIN L28
D2: 50S RIBOSOMAL PROTEIN L29
D3: 50S RIBOSOMAL PROTEIN L30
D4: 50S RIBOSOMAL PROTEIN L31
D5: 50S RIBOSOMAL PROTEIN L32
D6: 50S RIBOSOMAL PROTEIN L33
D7: 50S RIBOSOMAL PROTEIN L34
D8: 50S RIBOSOMAL PROTEIN L35
D9: 50S RIBOSOMAL PROTEIN L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,289,912636
Polymers2,275,16657
Non-polymers14,746579
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.459, 447.344, 622.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
RNA chain , 6 types, 14 molecules AACAAVCVAWAYCWCYAXCXBADABBDB

#1: RNA chain 16S rRNA


Mass: 493942.281 Da / Num. of mol.: 2 / Mutation: G299A / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#22: RNA chain P-SITE tRNA fMet


Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: GenBank: AP012306.1
#23: RNA chain
E-SITE TRNA PHE OR A-SITE tRNA Phe


Mass: 24485.539 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: GenBank: AP012306.1
#24: RNA chain mRNA


Mass: 7827.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide
#25: RNA chain 23S rRNA


Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#26: RNA chain 5S rRNA


Mass: 39494.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1

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

#2: Protein 30S ribosomal protein S2


Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371
#3: Protein 30S ribosomal protein S3


Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372
#4: Protein 30S ribosomal protein S4


Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373
#5: Protein 30S ribosomal protein S5


Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5
#6: Protein 30S ribosomal protein S6 / TS9


Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8
#7: Protein 30S ribosomal protein S7


Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291
#8: Protein 30S ribosomal protein S8


Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#9: Protein 30S ribosomal protein S9


Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374
#10: Protein 30S ribosomal protein S10


Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7
#11: Protein 30S ribosomal protein S11


Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376
#12: Protein 30S ribosomal protein S12


Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3
#13: Protein 30S ribosomal protein S13


Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377
#14: Protein 30S ribosomal protein S14 type Z


Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#15: Protein 30S ribosomal protein S15


Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76
#16: Protein 30S ribosomal protein S16


Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3
#17: Protein 30S ribosomal protein S17


Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#18: Protein 30S ribosomal protein S18


Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0
#19: Protein 30S ribosomal protein S19


Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2
#20: Protein 30S ribosomal protein S20


Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380
#21: Protein/peptide 30S ribosomal protein Thx / S31


Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3

+
50S RIBOSOMAL PROTEIN ... , 30 types, 60 molecules BCDCBDDDBEDEBFDFBGDGBHDHBIDIBNDNBODOBPDPBQDQBRDRBSDSBTDTBUDU...

#27: Protein 50S RIBOSOMAL PROTEIN L1


Mass: 24872.721 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP7
#28: Protein 50S RIBOSOMAL PROTEIN L2


Mass: 30532.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60405
#29: Protein 50S RIBOSOMAL PROTEIN L3


Mass: 22450.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN8
#30: Protein 50S RIBOSOMAL PROTEIN L4


Mass: 23271.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN9
#31: Protein 50S RIBOSOMAL PROTEIN L5


Mass: 21061.596 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ0
#32: Protein 50S RIBOSOMAL PROTEIN L6


Mass: 19568.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#33: Protein 50S RIBOSOMAL PROTEIN L9


Mass: 16422.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ1
#34: Protein 50S RIBOSOMAL PROTEIN L13


Mass: 15927.903 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60488
#35: Protein 50S RIBOSOMAL PROTEIN L14


Mass: 13323.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP8
#36: Protein 50S RIBOSOMAL PROTEIN L15


Mass: 16319.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ7
#37: Protein 50S RIBOSOMAL PROTEIN L16


Mass: 15993.909 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60489
#38: Protein 50S RIBOSOMAL PROTEIN L17


Mass: 13750.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q9Z9H5
#39: Protein 50S RIBOSOMAL PROTEIN L18


Mass: 12639.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ4
#40: Protein 50S RIBOSOMAL PROTEIN L19


Mass: 17188.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60490
#41: Protein 50S RIBOSOMAL PROTEIN L20


Mass: 13779.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60491
#42: Protein 50S RIBOSOMAL PROTEIN L21


Mass: 11069.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60492
#43: Protein 50S RIBOSOMAL PROTEIN L22


Mass: 12808.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP3
#44: Protein 50S RIBOSOMAL PROTEIN L23


Mass: 10759.808 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP0
#45: Protein 50S RIBOSOMAL PROTEIN L24


Mass: 12085.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP9
#46: Protein 50S RIBOSOMAL PROTEIN L25


Mass: 23238.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHZ1
#47: Protein 50S RIBOSOMAL PROTEIN L27


Mass: 9529.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60493
#48: Protein 50S RIBOSOMAL PROTEIN L28


Mass: 11004.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P60494
#49: Protein 50S RIBOSOMAL PROTEIN L29


Mass: 8670.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP6
#50: Protein 50S RIBOSOMAL PROTEIN L30


Mass: 6799.126 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ6
#51: Protein 50S RIBOSOMAL PROTEIN L31


Mass: 8300.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJE1
#52: Protein 50S RIBOSOMAL PROTEIN L32


Mass: 6722.050 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80339
#53: Protein 50S RIBOSOMAL PROTEIN L33


Mass: 6632.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P35871
#54: Protein/peptide 50S RIBOSOMAL PROTEIN L34


Mass: 6132.449 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80340
#55: Protein 50S RIBOSOMAL PROTEIN L35


Mass: 7506.178 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SKU1
#56: Protein/peptide 50S RIBOSOMAL PROTEIN L36


Mass: 4435.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHR2

-
Non-polymers , 3 types, 1039 molecules

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


Mass: 24.305 Da / Num. of mol.: 1033 / Source method: obtained synthetically / Formula: Mg
#58: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#59: Chemical
ChemComp-ZN / ZINC ION


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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN, 10mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2011 / Details: mirrors
RadiationMonochromator: KOHZU DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 720970 / Num. obs: 720017 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Rmerge(I) obs: 0.438 / Rsym value: 0.461 / Net I/σ(I): 6.3
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.303 / Mean I/σ(I) obs: 1.8 / Rsym value: 1.382 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.7_641)model building
PHENIX(phenix.refine: 1.7_641)refinement
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.7_641phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2WDG 2WDH 2WDI 2WDJ

2wdg
PDB Unreleased entry

2wdh
PDB Unreleased entry

2wdi
PDB Unreleased entry

2wdj
PDB Unreleased entry


Resolution: 3.516→35.071 Å / SU ML: 0.41 / σ(F): 1.99 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 32818 4.56 %
Rwork0.2102 --
obs0.2119 719893 99.86 %
all-720970 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4477 Å20 Å20 Å2
2--5.0433 Å2-0 Å2
3---5.6251 Å2
Refinement stepCycle: LAST / Resolution: 3.516→35.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19156 36211 501 0 55868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009319235
X-RAY DIFFRACTIONf_angle_d1.052477412
X-RAY DIFFRACTIONf_dihedral_angle_d20.121148976
X-RAY DIFFRACTIONf_chiral_restr0.08860525
X-RAY DIFFRACTIONf_plane_restr0.00825904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5158-3.55570.325911570.290521899X-RAY DIFFRACTION97
3.5557-3.59750.321311910.286322652X-RAY DIFFRACTION100
3.5975-3.64130.302911340.275122721X-RAY DIFFRACTION100
3.6413-3.68740.309411900.270822699X-RAY DIFFRACTION100
3.6874-3.73590.29911910.260322673X-RAY DIFFRACTION100
3.7359-3.7870.276211970.253422672X-RAY DIFFRACTION100
3.787-3.8410.278311860.245222745X-RAY DIFFRACTION100
3.841-3.89830.286711300.241222778X-RAY DIFFRACTION100
3.8983-3.95910.268811890.23322716X-RAY DIFFRACTION100
3.9591-4.02390.265811960.22722633X-RAY DIFFRACTION100
4.0239-4.09320.253611940.224522750X-RAY DIFFRACTION100
4.0932-4.16750.241411880.215822666X-RAY DIFFRACTION100
4.1675-4.24750.279611970.209522736X-RAY DIFFRACTION100
4.2475-4.33410.248211980.213322780X-RAY DIFFRACTION100
4.3341-4.42820.242911640.206722786X-RAY DIFFRACTION100
4.4282-4.5310.2545610.199923415X-RAY DIFFRACTION100
4.531-4.6440.23837040.200523259X-RAY DIFFRACTION100
4.644-4.76930.23978140.197923145X-RAY DIFFRACTION100
4.7693-4.90930.22249950.191723060X-RAY DIFFRACTION100
4.9093-5.06730.225911760.189822755X-RAY DIFFRACTION100
5.0673-5.24780.227811810.185522893X-RAY DIFFRACTION100
5.2478-5.45720.224611820.1822800X-RAY DIFFRACTION100
5.4572-5.70450.222811850.182622917X-RAY DIFFRACTION100
5.7045-6.00390.229611960.183322904X-RAY DIFFRACTION100
6.0039-6.3780.23211860.184522955X-RAY DIFFRACTION100
6.378-6.8670.2311940.185422915X-RAY DIFFRACTION100
6.867-7.55180.23337260.177823523X-RAY DIFFRACTION100
7.5518-8.63030.22718640.19123449X-RAY DIFFRACTION100
8.6303-10.82010.230410000.204223444X-RAY DIFFRACTION100
10.8201-35.07260.245111520.223823735X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0189-0.0101-0.00030.0450.00960.0326-0.0010.0401-0.0223-0.0113-0.0545-0.01290.04550.0057-0.07250.48270.1225-0.23860.382-0.16520.4067-11.095241.932597.7768
20.0002-0.00350.00730.006-0.01330.02670.00840.061-0.0009-0.042-0.012300.00240.0171-00.44810.0635-0.0520.36450.01940.247-13.4928115.992273.7442
30.0159-0.00250.0258-0.00260.00480.02350.00370.01330.006-0.0512-0.03480.06710.0036-0.0081-0.03810.35190.0604-0.27560.3497-0.08520.3635-88.8311102.129762.6155
40.00150.00590.00540.0240.02480.0198-0.01260.016-0.0041-0.00880.0076-0.00020.0033-0.0006-00.44510.0347-0.07780.4278-0.01450.4258-11.954982.5881113.6433
50.0002-0.00010.0004-00.00010.0003-0.001-0.00140.0004-0.001-0.0010.00030.0004-0.001100.53630.0066-0.0130.5371-0.00640.5311-45.349773.588252.9031
60-00.00010-00.00010.00020-00.00030.0002-0.0002-0.0003-0.0002-00.53840.006-0.00360.5363-0.00420.5357-23.174764.22856.155
70.0001-0.00020.00010.0001-0.00010.0001-0.0001-0.00030.0003-0.0003-0.0006-0.00020.0003-0.0004-00.57830.0056-0.00690.5794-0.00260.574-25.942167.444853.3766
80.00010.0001-0.00020-00.0001-0.00080.00040.0010.0007-0.00270.00030.0006-0-00.47690.0001-0.00080.4769-0.00320.4756-15.959575.11587.9669
90000.00030.00030.00030.0005-0-0.00030.0004-0.0007-0.00080.0001-0.0012-00.39220.0038-0.00870.3835-0.00940.392-44.211567.8195105.4238
100.00010.000100.000100-0.00020.0002-0.00010.0003-0.00040.0001-0.00030.000100.52270.0005-0.0050.52210.00060.5225-54.261751.619199.813
110.00010.00020.0001-0-0.000200.0004-0.0002-0.0001-0.00010.0002-0.00020.00060.000900.52670.0042-0.00290.52410.00210.523724.943.198126.8163
120.0001-0000.00010.0001-0.00010.00040.00020-0.0001-0.00010.0004-0-00.57410.0043-0.00270.5751-0.00060.574934.743243.7703118.6121
130.00010-00.000100.0001-0.00030.0003-0-0-0.0003-0.000200.0001-00.86870.0019-0.0010.8692-0.0010.870248.100652.9564117.2576
14-0.00080.0009-0.0011-0.0002-0.00050.0030.02680.01760.0063-0.00620.01-0.0040.00220.0083-00.57720.0308-0.00790.5633-0.01130.54872.796967.5371.6919
150.00950.0042-0.01460.0331-0.03780.0507-0.01570.05010.0271-0.0844-0.0194-0.0377-0.00940.01250.00280.40770.09280.07630.38230.23440.3237-64.435514.3576-69.4372
160.0056-0.0020.00570.04290.00920.0088-0.02850.00750.0850.01930.0126-0.0191-0.0396-0.001-0.00030.3818-0.0334-0.11490.1570.06680.3389-65.647437.14155.4358
170.0297-0.03240.01120.0344-0.01980.0058-0.0022-0.00490.02010.02770.03570.0138-0.0774-0.07980.01950.36220.19110.00560.3020.10730.4022-140.938149.7418-7.7482
18-0.0003-0.00360.00260.0192-0.02350.0213-0.03430.01890.01290.0004-0.0167-0.0135-0.02030.0152-00.29820.03220.0060.27380.03930.2895-64.7386-1.9204-28.7755
190.0002-0.0003-0.00010.0003-0.000200.0005-0.0007-0.0009-0.00050.002-0.0003-0.0010.000100.28890.0114-0.00280.28060.00980.2839-96.886859.2589-36.2922
20-00-00.0001-0.00010.00010.00010.0003-0.00020.00020.00030.00050.00040.0003-00.4862-0.001-0.00130.48310.00870.4856-75.193255.7083-46.1843
210.0002-0.0002-00.00020-0-0.0006-0.0006-0.0010.0004-0.00010.00140.0008-0.0001-00.38090.00030.00060.37770.01120.3815-78.232758.6978-42.6104
220.00010.000200.0001-00.0001-0.0003-0.00050.00110.0004-0.0003-0.0014-0.00080.000500.2106-0.003-0.00020.21410.00450.212-68.884323.6516-36.0816
230.00010-0.00010.0004-0.00040.0003-0.00080.00090.00090.0009-0.0006-0.00060.0002-0.000400.11930.00330.00090.10950.01470.1085-97.20267.035-43.134
240000.000100-00.0001-0.00030.0001-0-0.000300.0002-00.36230.0006-0.00460.36510.00370.3625-107.741413.4085-58.833
250.00010.0001-0.0002-0-0.00010.00020.00080.00080.000400.0012-0.001-0.0007-0.001100.50070.00320.00330.50230.00460.501-28.9815-15.2535-69.1552
2600-00-000.00050.00030.0002-0.00060.0009-0.00010.00020.0001-00.5218-0.00010.00390.52330.00250.5219-19.121-6.9031-68.9742
270.0001-0-00-00.0001-0-00.000400.00020.00020.00010.000200.77050.00190.00330.7734-0.00040.7725-5.0311-5.2697-59.3097
280.00110.0072-0.00050.0096-0.0030.0010.01490.00480.01440.0026-0.0048-0.0168-0.0050.00400.5294-0.02090.00250.51030.04660.5314-49.80139.7732-43.4139
290.00090.0005-0.00040.0011-0.00120.000900.00270.00210.00170.0032-0.00180.00330.003100.5084-0.01320.01320.54060.02120.5351-97.9994116.5351186.6755
300.00240.0008-0.0007-0.0001-0.0005-0-0.0041-0.00540.0006-0.00040.00220.00480.0022-0.000700.70320.00310.00170.76220.01850.7694-124.9459151.3209156.8486
310.00350.0056-0.00630.0077-0.01040.009-0.0133-0.0119-0.0045-0.0072-0.03230.0025-0.01340.007400.39950.0029-0.01340.38710.03110.3757-48.7223193.495997.2669
320.0001-0.0001-00.00030.00010.0001-0.0003-00.0011-0.00070.00010.0004-00.0003-00.4198-0.00030.00270.41110.00710.410810.9227231.631790.5453
330.00140.00110.00030.0014-0.0010.00120.0016-0.00120-0.0011-0.0053-0.00370.00160.005300.4301-0.0321-0.01290.4610.01260.4608-95.7139106.7935156.0884
340.1339-0.02910.13710.11890.00370.21680.0348-0.050.07880.09330.052-0.01480.0575-0.02080.28420.1274-0.0006-0.10710.15390.01960.089-17.0035132.0998170.7948
350.00050.0002-0.00010.00050.00070.00060.0027-0.0031-0.0031-0.00050.0009-0.00220.00060.0022-00.49310.0079-0.02260.5176-0.00430.5282-116.0553140.6478127.6341
360.00080.001-0.00010.001-0.00020.0007-0.0015-0.0009-0.0003-0.0015-0.0027-0.0010.00050.0013-00.2346-0.0321-0.01620.25460.01320.255-151.8575-73.68032.7031
370.0023-0.00040.0004-0.0001-0.00010.00030.0008-0.0005-0.0051-0.0001-0.00430.001-0.00110.0016-00.3906-0.0020.00080.45580.030.4441-178.6355-45.519238.4525
380.00350.00550.00580.00690.00910.0070.00690.0035-0.0070.01080.0203-0.0022-0.0053-0.000700.16160.0043-0.00780.1382-0.02950.1412-101.712812.302382.7806
390000.0002-0.00020.0003-0.0001-0.0003-0.001-0.0002-0.00050.00010.0007-0.0003-00.6394-0.0062-0.00790.6361-0.01080.6311-39.954819.739119.7673
400.00210.00040.00160.0023-00.0030.00420-0.00210.0019-0.0015-0.0036-0.00570.00320.00150.0421-0.0015-0.02750.05340.00460.0445-149.3688-43.1081-5.9714
410.0875-0.04430.08480.0729-0.08450.1214-0.0098-0.0671-0.0784-0.0355-0.0259-0.01110.1315-0.0169-0.0305-0.06010.0041-0.0784-0.07910.00750.0198-72.3123-59.744218.0456
420.0009-0.00040.00010.0009-0.00050.00030.00430.0021-0.00170.00010.00260.0007-0.0046-0.000200.29720.0103-0.00040.32940.01660.321-169.7873-16.059229.0389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain AA and (resid 4:576)) or (chain AD)
2X-RAY DIFFRACTION2((chain AA and ((resid 577:603) or (resid
3X-RAY DIFFRACTION3((chain AA and (resid 943:1417)) or (chain
4X-RAY DIFFRACTION4(chain AA and (resid 1418:1546))
5X-RAY DIFFRACTION5(chain AE and (resid 5:69))
6X-RAY DIFFRACTION6(chain AE and (resid 70:101))
7X-RAY DIFFRACTION7(chain AE and (resid 102:155))
8X-RAY DIFFRACTION8(chain AL and (resid 5:28))
9X-RAY DIFFRACTION9(chain AL and (resid 29:105))
10X-RAY DIFFRACTION10(chain AL and (resid 106:129))
11X-RAY DIFFRACTION11(chain AT and (resid 8:50))
12X-RAY DIFFRACTION12(chain AT and (resid 51:83))
13X-RAY DIFFRACTION13(chain AT and (resid 84:106))
14X-RAY DIFFRACTION14(chain AA and (resid 604:669))
15X-RAY DIFFRACTION15((chain CA and (resid 4:576)) or (chain CD)
16X-RAY DIFFRACTION16((chain CA and ((resid 577:603) or (resid
17X-RAY DIFFRACTION17((chain CA and (resid 943:1417)) or (chain
18X-RAY DIFFRACTION18(chain CA and (resid 1418:1546))
19X-RAY DIFFRACTION19(chain CE and (resid 5:69))
20X-RAY DIFFRACTION20(chain CE and (resid 70:101))
21X-RAY DIFFRACTION21(chain CE and (resid 102:155))
22X-RAY DIFFRACTION22(chain CL and (resid 5:28))
23X-RAY DIFFRACTION23(chain CL and (resid 29:105))
24X-RAY DIFFRACTION24(chain CL and (resid 106:129))
25X-RAY DIFFRACTION25(chain CT and (resid 8:50))
26X-RAY DIFFRACTION26(chain CT and (resid 51:83))
27X-RAY DIFFRACTION27(chain CT and (resid 84:106))
28X-RAY DIFFRACTION28(chain CA and (resid 604:669))
29X-RAY DIFFRACTION29((chain BB and (resid 70:107)) or (chain BZ
30X-RAY DIFFRACTION30((chain BB and (resid 1:69)) or (chain BB and
31X-RAY DIFFRACTION31((chain BA and (resid 2088:2227)) or (chain
32X-RAY DIFFRACTION32(chain BI and (resid 54:145))
33X-RAY DIFFRACTION33((chain BA and (resid 866:907)) or (chain BZ
34X-RAY DIFFRACTION34((chain BA and (resid 11:865)) or (chain BA
35X-RAY DIFFRACTION35((chain BA and (resid 2297:2319)) or (chain
36X-RAY DIFFRACTION36((chain DB and (resid 70:107)) or (chain DZ
37X-RAY DIFFRACTION37((chain DB and (resid 1:69)) or (chain DB and
38X-RAY DIFFRACTION38((chain DA and (resid 2088:2227)) or (chain
39X-RAY DIFFRACTION39(chain DI and (resid 54:145))
40X-RAY DIFFRACTION40((chain DA and (resid 866:907)) or (chain DZ
41X-RAY DIFFRACTION41((chain DA and (resid 11:865)) or (chain DA
42X-RAY DIFFRACTION42((chain DA and (resid 2297:2319)) or (chain

+
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