[English] 日本語
Yorodumi
- PDB-2otj: 13-deoxytedanolide bound to the large subunit of Haloarcula maris... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2otj
Title13-deoxytedanolide bound to the large subunit of Haloarcula marismortui
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / 13 deoxytedanolide / antibiotic complex / 50S
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / DNA repair / nucleotide binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 ...Single Heli x bin / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A - #60 / Ribosomal protein L30/L7, central domain / Ribosomal protein L39 / 50s Ribosomal Protein L19e, Chain O, domain 1 - #10 / N-terminal domain of TfIIb - #30 / Ribosomal protein L21 / Ribosomal Protein L31e; Chain: W; / Ribosomal protein L31 / Nuclear Transport Factor 2; Chain: A, - #80 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 / Molecule: Ribosomal Protein L15; Chain: K; domain 1 - #10 / 3-methyladenine DNA Glycosylase II; Chain A, domain 3 / Ribosomal protein L24 / Ribosomal protein L3; domain 3 / Ribosomal protein L3, domain 3 / Ribosomal protein L15e / Ribosomal protein L15 / Ribosomal Protein L15; Chain: K; domain 2 - #10 / Ribosomal Protein L3; Chain: B; domain 2, / Ribosomal Protein L3; Chain: B; domain 2, - #10 / Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 50s Ribosomal Protein L19e, Chain O, domain 1 / Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / Helix Hairpins - #310 / 50S ribosomal protein L10, archaea / Ribosomal Protein L13p; Chain: A; / Ribosomal protein L13 / Atp Synthase Epsilon Chain; Chain: I; / Ribosomal Protein L24e; Chain: T; / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L15e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L6 / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Outer Surface Protein A; domain 3 / Ribosomal protein L7Ae, archaea / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Ribosomal protein L24e / SH3 type barrels. - #30 / Ribosomal protein L30/S12 / Aldehyde Oxidoreductase; domain 3 / DNA repair Rad51/transcription factor NusA, alpha-helical / : / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / N-terminal domain of TfIIb / Helix-hairpin-helix domain / Ribosomal protein L2, archaeal-type / Translation factors / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / RRM (RNA recognition motif) domain / 60s Ribosomal Protein L30; Chain: A; / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Ribosomal protein L44e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e / Ribosomal protein L24e, conserved site / Ribosomal protein L44 / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature.
Similarity search - Domain/homology
13-DEOXYTEDANOLIDE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 ...13-DEOXYTEDANOLIDE / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBlaha, G. / Schroeder, S.J. / Tirado-Rives, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole.
Authors: Schroeder, S.J. / Blaha, G. / Tirado-Rives, J. / Steitz, T.A. / Moore, P.B.
History
DepositionFeb 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 23S ribosomal RNA
9: 5S ribosomal RNA
A: 50S ribosomal protein L2P
B: 50S ribosomal protein L3P
C: 50S ribosomal protein L4P
D: 50S ribosomal protein L5P
E: 50S ribosomal protein L6P
F: 50S ribosomal protein L7Ae
G: 50S ribosomal protein L10E
H: 50S ribosomal protein L10e
J: 50S ribosomal protein L13P
K: 50S ribosomal protein L14P
L: 50S ribosomal protein L15P
M: 50S ribosomal protein L15e
N: 50S ribosomal protein L18P
O: 50S ribosomal protein L18e
P: 50S ribosomal protein L19e
Q: 50S ribosomal protein L21e
R: 50S ribosomal protein L22P
S: 50S ribosomal protein L23P
T: 50S ribosomal protein L24P
U: 50S ribosomal protein L24e
V: 50S ribosomal protein L29P
W: 50S ribosomal protein L30P
X: 50S ribosomal protein L31e
Y: 50S ribosomal protein L32e
Z: 50S ribosomal protein L37Ae
1: 50S ribosomal protein L37e
2: 50S ribosomal protein L39e
3: 50S ribosomal protein L44E
I: 50S ribosomal protein L11P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,478,890264
Polymers1,472,05431
Non-polymers6,836233
Water140,2297784
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.738, 299.519, 573.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe asymmetric unit contains one 50S molecule, consisting of 2 rRNA and 29 ribosomal proteins.

-
Components

-
RNA chain , 2 types, 2 molecules 09

#1: RNA chain 23S ribosomal RNA


Mass: 946090.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: encoded by rRNA operons / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779
#2: RNA chain 5S ribosomal RNA


Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: encoded by rRNA operons / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779

+
50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHJKLMNOPQRSTUVWXYZ123I

#3: Protein 50S ribosomal protein L2P / Hmal2 / Hl4


Mass: 25354.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20276
#4: Protein 50S ribosomal protein L3P / Hmal3 / Hl1


Mass: 37396.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P20279
#5: Protein 50S ribosomal protein L4P / Hmal4 / Hl6


Mass: 26442.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12735
#6: Protein 50S ribosomal protein L5P / Hmal5 / Hl13


Mass: 19551.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14124
#7: Protein 50S ribosomal protein L6P / Hmal6 / Hl10


Mass: 19961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14135
#8: Protein 50S ribosomal protein L7Ae / Hs6


Mass: 12791.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12743
#9: Protein 50S ribosomal protein L10E / Ribosomal protein L10 / Acidic ribosomal protein P0 homolog / L10E / HMal10


Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825
#10: Protein 50S ribosomal protein L10e


Mass: 19068.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617
#11: Protein 50S ribosomal protein L13P / Hmal13


Mass: 16249.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P29198
#12: Protein 50S ribosomal protein L14P / Hmal14 / Hl27


Mass: 14191.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22450
#13: Protein 50S ribosomal protein L15P / Hmal15 / Hl9


Mass: 18005.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12737
#14: Protein 50S ribosomal protein L15e / 50S ribosomal protein LC12


Mass: 22157.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618
#15: Protein 50S ribosomal protein L18P / Hmal18 / Hl12


Mass: 20640.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14123
#16: Protein 50S ribosomal protein L18e / Hl29 / L19


Mass: 12438.915 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12733
#17: Protein 50S ribosomal protein L19e / Hmal19 / Hl24


Mass: 16796.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14119
#18: Protein 50S ribosomal protein L21e / Hl31


Mass: 10567.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12734
#19: Protein 50S ribosomal protein L22P / Hmal22 / Hl23


Mass: 16966.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10970
#20: Protein 50S ribosomal protein L23P / Hmal23 / Hl25 / L21


Mass: 9612.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12732
#21: Protein 50S ribosomal protein L24P / Hmal24 / Hl16 / Hl15


Mass: 13670.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10972
#22: Protein 50S ribosomal protein L24e / Hl21/Hl22


Mass: 7233.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14116
#23: Protein 50S ribosomal protein L29P / Hmal29 / Hl33


Mass: 7889.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P10971
#24: Protein 50S ribosomal protein L30P / Hmal30 / Hl20 / Hl16


Mass: 17062.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14121
#25: Protein 50S ribosomal protein L31e / L34 / Hl30


Mass: 10384.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P18138
#26: Protein 50S ribosomal protein L32e / Hl5


Mass: 26455.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P12736
#27: Protein 50S ribosomal protein L37Ae


Mass: 8294.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619
#28: Protein 50S ribosomal protein L37e / L35e


Mass: 6330.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32410
#29: Protein/peptide 50S ribosomal protein L39e / Hl39e / Hl46e


Mass: 6133.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P22452
#30: Protein 50S ribosomal protein L44E / La / Hla


Mass: 10815.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P32411
#31: Protein 50S ribosomal protein L11P / Hmal11


Mass: 16966.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P14122

-
Non-polymers , 7 types, 8017 molecules

#32: Chemical ChemComp-13T / 13-DEOXYTEDANOLIDE


Mass: 594.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H50O10
#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 117 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#35: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Na
#36: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#37: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7784 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEG 6000, KCl, NH4Cl, MGCl2, KAcetate, pH 5.8, vapor diffusion, sitting drop, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2KCl11
3NH4Cl11
4MGCl211
5H2O11
6PEG 600012
7KCl12
8NH4Cl12
9MGCl212

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2005
Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 422741 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.163 / Χ2: 1.003 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.85-2.924.9296800.9131,298.5
2.92-36.8299910.921,21000.98
3-3.097.3300660.9561,21000.692
3.09-3.197.3300601.0151,21000.488
3.19-3.37.3300951.0031,21000.357
3.3-3.437.3300921.0691,21000.281
3.43-3.597.3301641.0651,21000.229
3.59-3.787.3300981.0281,21000.186
3.78-4.027.3301780.9621,21000.154
4.02-4.337.3302001.0861,21000.134
4.33-4.767.2302591.0271,21000.12
4.76-5.457.2303681.0691,21000.113
5.45-6.867.1304750.9611,21000.106
6.86-506.9310150.9211,299.70.092

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S72

1s72


Resolution: 2.9→49.7 Å / Rfactor Rfree error: 0.004 / FOM work R set: 0.836 / Data cutoff high absF: 5165605.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.04 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3880 1 %RANDOM
Rwork0.193 ---
all-422741 --
obs-397264 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.687 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å20 Å20 Å2
2---2.65 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29364 61621 274 7784 99043
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.9
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it0.741.5
X-RAY DIFFRACTIONc_mcangle_it1.342
X-RAY DIFFRACTIONc_scbond_it0.842
X-RAY DIFFRACTIONc_scangle_it1.342.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.9-2.920.435770.39977027779
2.92-2.940.417770.35878147891
2.94-2.960.386710.34578337904
2.96-2.980.33860.32477767862
2.98-30.373740.31578447918
3-3.030.38740.30678237897
3.03-3.050.406780.29378577935
3.05-3.070.319870.27677387825
3.07-3.10.358740.26478467920
3.1-3.120.267760.24978357911
3.12-3.150.312710.24978687939
3.15-3.180.262710.21877837854
3.18-3.210.282940.22678317925
3.21-3.240.312760.22677967872
3.24-3.270.258800.21178907970
3.27-3.30.286760.21877907866
3.3-3.330.274540.22179097963
3.33-3.370.273760.21478067882
3.37-3.40.249810.20578557936
3.4-3.440.236830.20878277910
3.44-3.480.232660.19578337899
3.48-3.520.237740.19679027976
3.52-3.560.241770.19777917868
3.56-3.610.304630.19778597922
3.61-3.650.254840.18578917975
3.65-3.70.215790.1877797858
3.7-3.760.229790.16978557934
3.76-3.810.204800.16979007980
3.81-3.870.262670.17678677934
3.87-3.940.259820.17878427924
3.94-40.232740.15978507924
4-4.080.199810.16478937974
4.08-4.150.213870.16678457932
4.15-4.240.202780.14978467924
4.24-4.330.202830.14578667949
4.33-4.430.197840.15678687952
4.43-4.540.212640.14978577921
4.54-4.670.165900.15479067996
4.67-4.80.199770.1578907967
4.8-4.960.179750.14578967971
4.96-5.130.167890.14978627951
5.13-5.340.221800.15478997979
5.34-5.580.22750.15579298004
5.58-5.880.212710.16379558026
5.88-6.240.227830.17479198002
6.24-6.730.205690.17179388007
6.73-7.40.22790.16579658044
7.4-8.470.216970.18680048101
8.47-10.650.212790.20180488127
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2rna_ribo_modnts.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5dot.par&_1_TOPOLOGY_INFILE_5

+
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