[English] 日本語
Yorodumi
- PDB-5jc8: Crystal structure of a putative short-chain dehydrogenase/reducta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jc8
TitleCrystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia xenovorans
ComponentsPutative short-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid biosynthetic process
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a putative short-chain dehydrogenase/reductase from Burkholderia xenovorans
Authors: Conrady, D.G. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative short-chain dehydrogenase/reductase
B: Putative short-chain dehydrogenase/reductase
C: Putative short-chain dehydrogenase/reductase
D: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,34122
Polymers115,2284
Non-polymers1,11318
Water19,0601058
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint-110 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.180, 81.080, 86.370
Angle α, β, γ (deg.)90.000, 94.530, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4:12 or resid 14:18 or resid...
21(chain B and (resid 4:12 or resid 14:18 or resid...
31(chain C and (resid 4:12 or resid 14:18 or resid...
41(chain D and (resid 4:12 or resid 14:18 or resid...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAALAALA(chain A and (resid 4:12 or resid 14:18 or resid...AA4 - 1212 - 20
12VALVALGLYGLY(chain A and (resid 4:12 or resid 14:18 or resid...AA14 - 1822 - 26
13GLYGLYASPASP(chain A and (resid 4:12 or resid 14:18 or resid...AA21 - 4529 - 53
14ASPASPLEULEU(chain A and (resid 4:12 or resid 14:18 or resid...AA47 - 5555 - 63
15LEULEUPROPRO(chain A and (resid 4:12 or resid 14:18 or resid...AA57 - 6765 - 75
16LEULEUVALVAL(chain A and (resid 4:12 or resid 14:18 or resid...AA69 - 7877 - 86
17LEULEUALAALA(chain A and (resid 4:12 or resid 14:18 or resid...AA81 - 8789 - 95
18CYSCYSGLYGLY(chain A and (resid 4:12 or resid 14:18 or resid...AA89 - 9097 - 98
19VALVALASNASN(chain A and (resid 4:12 or resid 14:18 or resid...AA92 - 98100 - 106
110GLYGLYPROPRO(chain A and (resid 4:12 or resid 14:18 or resid...AA100 - 102108 - 110
111PROPROLEULEU(chain A and (resid 4:12 or resid 14:18 or resid...AA104 - 110112 - 118
112GLUGLUALAALA(chain A and (resid 4:12 or resid 14:18 or resid...AA112 - 116120 - 124
113GLNGLNGLUGLU(chain A and (resid 4:12 or resid 14:18 or resid...AA118 - 138126 - 146
114GLNGLNGLNGLN(chain A and (resid 4:12 or resid 14:18 or resid...AA139147
115ALAALAASPASP(chain A and (resid 4:12 or resid 14:18 or resid...AA4 - 26812 - 276
116ALAALAASPASP(chain A and (resid 4:12 or resid 14:18 or resid...AA4 - 26812 - 276
117ALAALAASPASP(chain A and (resid 4:12 or resid 14:18 or resid...AA4 - 26812 - 276
118ALAALAASPASP(chain A and (resid 4:12 or resid 14:18 or resid...AA4 - 26812 - 276
21ALAALAALAALA(chain B and (resid 4:12 or resid 14:18 or resid...BB4 - 1212 - 20
22VALVALGLYGLY(chain B and (resid 4:12 or resid 14:18 or resid...BB14 - 1822 - 26
23GLYGLYASPASP(chain B and (resid 4:12 or resid 14:18 or resid...BB21 - 4529 - 53
24ASPASPLEULEU(chain B and (resid 4:12 or resid 14:18 or resid...BB47 - 5555 - 63
25LEULEUPROPRO(chain B and (resid 4:12 or resid 14:18 or resid...BB57 - 6765 - 75
26LEULEUVALVAL(chain B and (resid 4:12 or resid 14:18 or resid...BB69 - 7877 - 86
27LEULEUALAALA(chain B and (resid 4:12 or resid 14:18 or resid...BB81 - 8789 - 95
28CYSCYSGLYGLY(chain B and (resid 4:12 or resid 14:18 or resid...BB89 - 9097 - 98
29VALVALASNASN(chain B and (resid 4:12 or resid 14:18 or resid...BB92 - 98100 - 106
210GLYGLYPROPRO(chain B and (resid 4:12 or resid 14:18 or resid...BB100 - 102108 - 110
211PROPROLEULEU(chain B and (resid 4:12 or resid 14:18 or resid...BB104 - 110112 - 118
212GLUGLUALAALA(chain B and (resid 4:12 or resid 14:18 or resid...BB112 - 116120 - 124
213GLNGLNGLUGLU(chain B and (resid 4:12 or resid 14:18 or resid...BB118 - 138126 - 146
214GLNGLNGLNGLN(chain B and (resid 4:12 or resid 14:18 or resid...BB139147
215ALAALAASPASP(chain B and (resid 4:12 or resid 14:18 or resid...BB4 - 26812 - 276
216ALAALAASPASP(chain B and (resid 4:12 or resid 14:18 or resid...BB4 - 26812 - 276
217ALAALAASPASP(chain B and (resid 4:12 or resid 14:18 or resid...BB4 - 26812 - 276
218ALAALAASPASP(chain B and (resid 4:12 or resid 14:18 or resid...BB4 - 26812 - 276
31ALAALAALAALA(chain C and (resid 4:12 or resid 14:18 or resid...CC4 - 1212 - 20
32VALVALGLYGLY(chain C and (resid 4:12 or resid 14:18 or resid...CC14 - 1822 - 26
33GLYGLYASPASP(chain C and (resid 4:12 or resid 14:18 or resid...CC21 - 4529 - 53
34ASPASPLEULEU(chain C and (resid 4:12 or resid 14:18 or resid...CC47 - 5555 - 63
35LEULEUPROPRO(chain C and (resid 4:12 or resid 14:18 or resid...CC57 - 6765 - 75
36LEULEUVALVAL(chain C and (resid 4:12 or resid 14:18 or resid...CC69 - 7877 - 86
37LEULEUALAALA(chain C and (resid 4:12 or resid 14:18 or resid...CC81 - 8789 - 95
38CYSCYSGLYGLY(chain C and (resid 4:12 or resid 14:18 or resid...CC89 - 9097 - 98
39VALVALASNASN(chain C and (resid 4:12 or resid 14:18 or resid...CC92 - 98100 - 106
310GLYGLYPROPRO(chain C and (resid 4:12 or resid 14:18 or resid...CC100 - 102108 - 110
311PROPROLEULEU(chain C and (resid 4:12 or resid 14:18 or resid...CC104 - 110112 - 118
312GLUGLUALAALA(chain C and (resid 4:12 or resid 14:18 or resid...CC112 - 116120 - 124
313GLNGLNTHRTHR(chain C and (resid 4:12 or resid 14:18 or resid...CC118 - 151126 - 159
314GLYGLYPROPRO(chain C and (resid 4:12 or resid 14:18 or resid...CC153 - 200161 - 208
315VALVALLEULEU(chain C and (resid 4:12 or resid 14:18 or resid...CC202 - 219210 - 227
316LYSLYSLYSLYS(chain C and (resid 4:12 or resid 14:18 or resid...CC221229
317ALAALAASPASP(chain C and (resid 4:12 or resid 14:18 or resid...CC4 - 26812 - 276
318ALAALAASPASP(chain C and (resid 4:12 or resid 14:18 or resid...CC4 - 26812 - 276
319ALAALAASPASP(chain C and (resid 4:12 or resid 14:18 or resid...CC4 - 26812 - 276
320ALAALAASPASP(chain C and (resid 4:12 or resid 14:18 or resid...CC4 - 26812 - 276
41ALAALAALAALA(chain D and (resid 4:12 or resid 14:18 or resid...DD4 - 1212 - 20
42VALVALGLYGLY(chain D and (resid 4:12 or resid 14:18 or resid...DD14 - 1822 - 26
43GLYGLYASPASP(chain D and (resid 4:12 or resid 14:18 or resid...DD21 - 4529 - 53
44ASPASPLEULEU(chain D and (resid 4:12 or resid 14:18 or resid...DD47 - 5555 - 63
45LEULEUPROPRO(chain D and (resid 4:12 or resid 14:18 or resid...DD57 - 6765 - 75
46LEULEUVALVAL(chain D and (resid 4:12 or resid 14:18 or resid...DD69 - 7877 - 86
47LEULEUALAALA(chain D and (resid 4:12 or resid 14:18 or resid...DD81 - 8789 - 95
48CYSCYSGLYGLY(chain D and (resid 4:12 or resid 14:18 or resid...DD89 - 9097 - 98
49VALVALASNASN(chain D and (resid 4:12 or resid 14:18 or resid...DD92 - 98100 - 106
410GLYGLYPROPRO(chain D and (resid 4:12 or resid 14:18 or resid...DD100 - 102108 - 110
411PROPROLEULEU(chain D and (resid 4:12 or resid 14:18 or resid...DD104 - 110112 - 118
412GLUGLUALAALA(chain D and (resid 4:12 or resid 14:18 or resid...DD112 - 116120 - 124
413GLNGLNGLUGLU(chain D and (resid 4:12 or resid 14:18 or resid...DD118 - 138126 - 146
414GLNGLNGLNGLN(chain D and (resid 4:12 or resid 14:18 or resid...DD139147
415ALAALAASPASP(chain D and (resid 4:12 or resid 14:18 or resid...DD4 - 26812 - 276
416ALAALAASPASP(chain D and (resid 4:12 or resid 14:18 or resid...DD4 - 26812 - 276
417ALAALAASPASP(chain D and (resid 4:12 or resid 14:18 or resid...DD4 - 26812 - 276
418ALAALAASPASP(chain D and (resid 4:12 or resid 14:18 or resid...DD4 - 26812 - 276

-
Components

#1: Protein
Putative short-chain dehydrogenase/reductase


Mass: 28807.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_C0972 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13GE3
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1058 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Rigaku Reagents JCSG+ screen H11: 0.2 M Magnesium Chloride, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350, BuxeA.00010.c.B1 PS02595 at 22.5mg/ml, cryo protected in 80% mother liquor-20% ethylene glycol mix

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→38.023 Å / Num. obs: 165687 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 12.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.038 / Net I/σ(I): 25.1
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.490.3514.45184.8
1.49-1.530.2666.13194.8
1.53-1.570.2157.42194.9
1.57-1.620.1749.22195.3
1.62-1.670.14510.81195.5
1.67-1.730.12112.8196
1.73-1.80.09715.66196.1
1.8-1.870.07918.67196.5
1.87-1.960.06322.89196.8
1.96-2.050.05127.36197.1
2.05-2.160.04331.93197.4
2.16-2.290.03537.88197.7
2.29-2.450.03340.38197.9
2.45-2.650.0343.87198.1
2.65-2.90.02847.29198.4
2.9-3.240.02652.77198.4
3.24-3.740.02257.92198.6
3.74-4.590.0261.21198.7
4.59-6.480.0260.76199
6.480.01959.94193.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXdev_2356refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NI5

4ni5


Resolution: 1.45→38.023 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1
RfactorNum. reflection% reflection
Rfree0.1576 2032 1.23 %
Rwork0.1411 --
obs0.1413 165652 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.57 Å2 / Biso mean: 18.9925 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.45→38.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7374 0 70 1068 8512
Biso mean--32.87 31.52 -
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077737
X-RAY DIFFRACTIONf_angle_d0.87810533
X-RAY DIFFRACTIONf_chiral_restr0.0791242
X-RAY DIFFRACTIONf_plane_restr0.0071395
X-RAY DIFFRACTIONf_dihedral_angle_d15.6112830
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3886X-RAY DIFFRACTION4.566TORSIONAL
12B3886X-RAY DIFFRACTION4.566TORSIONAL
13C3886X-RAY DIFFRACTION4.566TORSIONAL
14D3886X-RAY DIFFRACTION4.566TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.48370.20271120.19449476958884
1.4837-1.52080.18791260.164107321085895
1.5208-1.56190.18621040.1514108031090795
1.5619-1.60790.16911350.1391108221095795
1.6079-1.65980.15191160.1368108681098496
1.6598-1.71910.13771270.1344108541098196
1.7191-1.78790.16161260.139109201104696
1.7879-1.86930.17811510.1428109691112096
1.8693-1.96790.16061280.1402110531118197
1.9679-2.09110.18041310.1402110311116297
2.0911-2.25260.1431620.1387110821124498
2.2526-2.47920.16541560.1406111541131098
2.4792-2.83790.15321710.148111971136898
2.8379-3.5750.15871330.1372113031143699
3.575-38.0360.14291540.1351113561151098
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)
12.5771-0.4588-0.54073.26290.46452.4107-0.0445-0.1312-0.1420.0790.06930.10740.1123-0.1277-0.0230.0555-0.0183-0.0010.08560.02280.1241-41.9453-16.229429.5246
24.5926-0.4190.80681.2402-0.1231.24780.0296-0.2711-0.35460.0814-0.00560.11630.0643-0.0746-0.04740.1132-0.00940.01860.1220.03790.1531-44.0986-20.181735.2951
38.59743.60665.55462.7853.29014.51530.1336-0.3492-0.61250.1742-0.13780.00740.5752-0.251-0.09880.1795-0.02020.00680.11320.05380.2945-33.9012-31.24731.899
41.87811.04681.06172.07211.31262.01030.0297-0.118-0.1860.04090.0039-0.02340.1271-0.0324-0.03780.07640.00710.00830.07360.03720.11-25.8161-17.812234.3048
51.78861.61571.38281.8970.9341.6951-0.04640.007-0.03630.00530.1148-0.0833-0.05660.0689-0.04430.05690.01450.00380.05780.00550.0701-26.0473-5.672730.6335
61.53390.18870.10650.64220.33461.9356-0.01050.0215-0.1249-0.01090.0301-0.01130.10450.0128-0.01750.0653-0.0039-0.00530.0460.01070.0849-24.9974-11.912325.8788
70.8719-0.41950.4717.56680.93092.1264-0.0023-0.39980.2261.0970.1362-0.47220.0463-0.0897-0.08490.3490.0275-0.0360.3158-0.03550.2651-36.7572-0.366445.1607
82.08661.5495-0.14283.26920.44564.43190.1192-0.11150.21060.2909-0.03080.1561-0.2014-0.0014-0.05540.11090.03470.01150.1095-0.01180.143-36.4248.256235.2323
90.8563-0.1684-0.23591.08840.16130.8536-0.02020.0646-0.0192-0.01740.00220.04840.0143-0.03090.02440.07270.0039-0.01830.08240.00750.082-32.2982-4.657121.2569
101.02860.05370.07110.2847-0.10290.46040.0056-0.1171-0.11010.0261-0.0115-0.06030.04160.0680.00010.08240.0226-0.00930.10190.01060.0878-1.7382-7.529838.4666
111.57940.02970.10690.94030.16821.6976-0.00230.1427-0.177-0.05710.0103-0.0740.21120.1511-0.00390.08550.01530.00750.08640.00430.0844-1.575-4.248722.9769
122.32590.32750.32414.9338-0.0592.38220.11810.273-0.0973-0.3774-0.00180.09360.0185-0.0126-0.10490.11630.0346-0.08510.16070.00250.0682-40.38-0.40472.2857
131.9655-0.72720.75043.596-1.03472.85650.06320.3202-0.0496-0.3373-0.03560.10250.01920.0208-0.0350.12990.0102-0.05260.1586-0.00990.1018-40.63570.60920.1524
141.88670.24010.04991.59630.35491.5375-0.02090.254-0.0015-0.2725-0.01180.17190.106-0.06760.02950.21830.0422-0.04840.22640.04560.1337-42.10238.7754-3.3016
157.159-0.2933-1.22730.39250.22181.2280.00450.52140.0447-0.1234-0.0010.0083-0.0692-0.0491-0.05210.14280.0135-0.01720.1210.02250.0755-26.46377.00532.0156
162.2272-0.298-0.20091.0377-0.04920.5618-0.02530.20090.1453-0.05920.03320.0184-0.0571-0.0006-0.01340.12050.0034-0.01950.10810.01240.0615-26.46319.46025.8386
174.6812-1.1049-4.41370.95961.6145.50880.11540.21310.1477-0.0806-0.06380.0141-0.2041-0.1355-0.01330.10210.0086-0.02710.07230.01950.0865-26.22359.972813.5444
180.93220.57460.50351.8758-0.75241.0640.06760.5547-0.1236-0.2752-0.0702-0.15680.1777-0.08660.00390.11290.0118-0.02040.2022-0.03450.0964-28.8706-1.99366.0008
192.0466-0.30640.32971.380.14851.02880.0340.2795-0.2415-0.177-0.0189-0.0340.0980.0843-0.01410.1283-0.0077-0.00960.1007-0.00530.095-27.4873-8.197910.8618
202.19940.2115-0.26353.1332-0.47453.68720.00690.07160.2484-0.0241-0.0038-0.0506-0.28820.1998-0.00130.1215-0.06310.02010.12860.0090.12463.548621.074517.5504
211.83020.78820.15482.4740.55391.4603-0.08980.27610.28960.09150.0947-0.1491-0.32740.48240.05550.2337-0.06880.02220.20330.03210.223.948227.260413.1863
221.74720.2435-0.22980.777-0.24051.11610.01260.19650.3066-0.1301-0.0078-0.106-0.13580.2098-0.02250.158-0.040.01280.14110.02690.1221-4.111719.35956.9375
232.3328-0.0678-0.58090.6921-0.0421.484-0.02060.20390.1194-0.09050.0227-0.0082-0.06340.0579-0.0010.12-0.0206-0.00590.08280.01210.0799-10.538614.58819.4651
245.0035-4.5339-0.74455.97741.40441.15630.07040.21230.1258-0.1812-0.0068-0.1503-0.0390.1148-0.07550.1032-0.0162-0.00160.11180.01090.0615-10.54076.91629.8997
251.51870.1474-0.06631.63710.16061.75920.08440.09810.2536-0.0376-0.11290.1429-0.331-0.19520.02550.11440.006-0.00170.10120.02310.0981-10.483219.784322.0646
261.4333-0.7936-1.09491.59541.12091.62090.0243-0.04590.0781-0.0332-0.02160.0102-0.09560.0509-0.00580.0862-0.0049-0.0180.08050.00990.065-9.024113.267327.8684
273.08643.14951.10563.52081.83932.0490.3552-0.28530.00140.5303-0.1128-0.24090.44080.2263-0.28020.15060.0037-0.00670.1594-0.00310.1387-24.91058.590734.0408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 48 )A4 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 74 )A49 - 74
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 89 )A75 - 89
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 140 )A90 - 140
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 161 )A141 - 161
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 199 )A162 - 199
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 214 )A200 - 214
8X-RAY DIFFRACTION8chain 'A' and (resid 215 through 233 )A215 - 233
9X-RAY DIFFRACTION9chain 'A' and (resid 234 through 268 )A234 - 268
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 185 )B4 - 185
11X-RAY DIFFRACTION11chain 'B' and (resid 186 through 268 )B186 - 268
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 25 )C4 - 25
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 48 )C26 - 48
14X-RAY DIFFRACTION14chain 'C' and (resid 49 through 89 )C49 - 89
15X-RAY DIFFRACTION15chain 'C' and (resid 90 through 111 )C90 - 111
16X-RAY DIFFRACTION16chain 'C' and (resid 112 through 161 )C112 - 161
17X-RAY DIFFRACTION17chain 'C' and (resid 162 through 185 )C162 - 185
18X-RAY DIFFRACTION18chain 'C' and (resid 186 through 218 )C186 - 218
19X-RAY DIFFRACTION19chain 'C' and (resid 219 through 268 )C219 - 268
20X-RAY DIFFRACTION20chain 'D' and (resid 4 through 48 )D4 - 48
21X-RAY DIFFRACTION21chain 'D' and (resid 49 through 74 )D49 - 74
22X-RAY DIFFRACTION22chain 'D' and (resid 75 through 111 )D75 - 111
23X-RAY DIFFRACTION23chain 'D' and (resid 112 through 161 )D112 - 161
24X-RAY DIFFRACTION24chain 'D' and (resid 162 through 185 )D162 - 185
25X-RAY DIFFRACTION25chain 'D' and (resid 186 through 214 )D186 - 214
26X-RAY DIFFRACTION26chain 'D' and (resid 215 through 266 )D215 - 266
27X-RAY DIFFRACTION27chain 'D' and (resid 267 through 268 )D267 - 268

+
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