[English] 日本語
Yorodumi
- PDB-5ofq: Crystal structure of substrate-free CYP109A2 from Bacillus megaterium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ofq
TitleCrystal structure of substrate-free CYP109A2 from Bacillus megaterium
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Bacterial Proteins / Bacillus Megaterium / Bacillus / Cytochrome P-450 Enzyme System / Cytochrome P450 / Hydroxylation / Heme / Oxidation-Reduction / 25-Hydroxyvitamin D3 / Biocatalysis / Calcifediol / Cholecalciferol
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsJozwik, I.K. / Thunnissen, A.M.W.H.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission289217 Netherlands
CitationJournal: FEBS J. / Year: 2017
Title: Biochemical and structural characterization of CYP109A2, a vitamin D3 25-hydroxylase from Bacillus megaterium.
Authors: Abdulmughni, A. / Jozwik, I.K. / Brill, E. / Hannemann, F. / Thunnissen, A.W.H. / Bernhardt, R.
History
DepositionJul 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cytochrome P450
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,89116
Polymers187,9464
Non-polymers3,94612
Water27015
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2726
Polymers46,9861
Non-polymers1,2855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9374
Polymers46,9861
Non-polymers9513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0794
Polymers46,9861
Non-polymers1,0933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6032
Polymers46,9861
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.125, 155.534, 158.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 17:18 or resseq 20:21 or resseq...
21(chain B and (resseq 17:18 or resseq 20:21 or resseq...
31(chain C and (resseq 17:18 or resseq 20:21 or resseq...
41(chain D and (resseq 17:18 or resseq 20:21 or resseq...

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
11PROPROMETMET(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA17 - 1817 - 18
12GLUGLUILEILE(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA20 - 2120 - 21
13SERSERVALVAL(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA23 - 2423 - 24
14GLNGLNGLNGLN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA26 - 3926 - 39
15ALAALATYRTYR(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA41 - 5741 - 57
16THRTHRLEULEU(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA59 - 6459 - 64
17LYSLYSLYSLYS(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA6565
18ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
19ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
110ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
111ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
112ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
113ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
114ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
115ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
116ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
117ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
118ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
119ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
120ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
121ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
122ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
123ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
124ILEILEASNASN(chain A and (resseq 17:18 or resseq 20:21 or resseq...AA16 - 40116 - 401
21PROPROMETMET(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB17 - 1817 - 18
22GLUGLUILEILE(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB20 - 2120 - 21
23SERSERVALVAL(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB23 - 2423 - 24
24GLNGLNGLNGLN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB26 - 3926 - 39
25ALAALATYRTYR(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB41 - 5741 - 57
26THRTHRLEULEU(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB59 - 6459 - 64
27LYSLYSLYSLYS(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB6565
28ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
29ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
210ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
211ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
212ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
213ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
214ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
215ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
216ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
217ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
218ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
219ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
220ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
221ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
222ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
223ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
224ILEILEASNASN(chain B and (resseq 17:18 or resseq 20:21 or resseq...BB16 - 40116 - 401
31PROPROMETMET(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC17 - 1817 - 18
32GLUGLUILEILE(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC20 - 2120 - 21
33SERSERVALVAL(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC23 - 2423 - 24
34GLNGLNGLNGLN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC26 - 3926 - 39
35ALAALATYRTYR(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC41 - 5741 - 57
36THRTHRLEULEU(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC59 - 6459 - 64
37LYSLYSLYSLYS(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC6565
38ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
39ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
310ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
311ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
312ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
313ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
314ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
315ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
316ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
317ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
318ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
319ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
320ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
321ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
322ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
323ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
324ILEILEASNASN(chain C and (resseq 17:18 or resseq 20:21 or resseq...CC16 - 40116 - 401
41PROPROMETMET(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD17 - 1817 - 18
42GLUGLUILEILE(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD20 - 2120 - 21
43SERSERVALVAL(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD23 - 2423 - 24
44GLNGLNGLNGLN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD26 - 3926 - 39
45ALAALATYRTYR(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD41 - 5741 - 57
46THRTHRLEULEU(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD59 - 6459 - 64
47LYSLYSLYSLYS(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD6565
48LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
49LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
410LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
411LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
412LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
413LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
414LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
415LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
416LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
417LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
418LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
419LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
420LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
421LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
422LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
423LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401
424LEULEUASNASN(chain D and (resseq 17:18 or resseq 20:21 or resseq...DD15 - 40115 - 401

-
Components

#1: Protein
Cytochrome P450


Mass: 46986.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (strain DSM 319) (bacteria)
Gene: BMD_2035 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: D5DF88, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.9M ammonium sulfate, 0.1M HEPES pH 7.5, 2% (v/v) PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→52.03 Å / Num. obs: 51368 / % possible obs: 97.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 48.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.124 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.785.71.0250.5230.4581.12698.5
11.13-52.035.60.0260.9990.0110.02891.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.75 Å49.93 Å
Translation2.75 Å49.93 Å

-
Processing

Software
NameVersionClassification
EDNAdata collection
XDSdata reduction
Aimless0.2.8data scaling
PHASER2.5.5phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5l90

5l90


Resolution: 2.7→49.927 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.2751 5009 5.1 %
Rwork0.2238 --
obs0.2264 51368 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.67 Å2 / Biso mean: 45.9872 Å2 / Biso min: 29.6 Å2
Refinement stepCycle: final / Resolution: 2.7→49.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12444 0 267 15 12726
Biso mean--48.53 38.58 -
Num. residues----1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01812987
X-RAY DIFFRACTIONf_angle_d1.41817571
X-RAY DIFFRACTIONf_chiral_restr0.071886
X-RAY DIFFRACTIONf_plane_restr0.012273
X-RAY DIFFRACTIONf_dihedral_angle_d15.9434908
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8512X-RAY DIFFRACTION7.763TORSIONAL
12B8512X-RAY DIFFRACTION7.763TORSIONAL
13C8512X-RAY DIFFRACTION7.763TORSIONAL
14D8512X-RAY DIFFRACTION7.763TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.73070.40781700.40833190336099
2.7307-2.76280.42531810.38543130331199
2.7628-2.79650.37631710.36223133330499
2.7965-2.83190.4541980.34523079327798
2.8319-2.86910.35091430.34023215335899
2.8691-2.90840.39131720.31423110328298
2.9084-2.950.34691740.29263115328998
2.95-2.9940.351620.29173135329798
2.994-3.04080.37341840.2863126331098
3.0408-3.09060.32011790.28443129330898
3.0906-3.14390.3371570.28733088324598
3.1439-3.20110.36291410.28213168330998
3.2011-3.26260.36521500.29013157330798
3.2626-3.32920.35291640.25883123328798
3.3292-3.40160.29781670.24453135330298
3.4016-3.48070.27711950.23343060325598
3.4807-3.56770.28831700.23133100327097
3.5677-3.66420.30351700.22343127329797
3.6642-3.7720.27411770.20933098327598
3.772-3.89370.26111820.21043075325797
3.8937-4.03280.25011720.1983107327997
4.0328-4.19420.25641150.19423120323597
4.1942-4.38490.22021810.19143056323797
4.3849-4.6160.25792010.17693072327397
4.616-4.90490.1941560.17273092324896
4.9049-5.28330.19161510.17633067321896
5.2833-5.81420.21781560.19153064322096
5.8142-6.65390.24211550.18443072322796
6.6539-8.37670.20841510.16283057320895
8.3767-49.93560.19291640.16362987315194

+
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