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- PDB-7kkg: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant w... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7kkg
TitleDihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Components4-hydroxy-tetrahydrodipicolinate synthase
KeywordsLYASE / DIHYDRODIPICOLINATE SYNTHASE
Function / homology
Function and homology information


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsSaran, S. / Majdi Yazdi, M. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: A TIGHT DIMER INTERFACE N84 RESIDUE, PLAYS A CRITICAL ROLE IN THE TRANSMISSION OF THE ALLOSTERIC INHIBITION SIGNALS IN Cj.DHDPS
Authors: Saran, S. / Majdi Yazd, M. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionOct 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,27562
Polymers205,1176
Non-polymers4,15856
Water39,6152199
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,32432
Polymers136,7454
Non-polymers2,57928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14120 Å2
ΔGint-96 kcal/mol
Surface area40780 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,61346
Polymers136,7454
Non-polymers2,86842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16340 Å2
ΔGint-142 kcal/mol
Surface area40210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.670, 225.730, 200.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-613-

HOH

21F-461-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5:20 or resid 22:24 or resid...
21(chain B and (resid 5:20 or resid 22:24 or resid...
31(chain C and (resid 5:20 or resid 22:24 or resid...
41(chain D and (resid 5:20 or resid 22:24 or resid...
51(chain E and (resid 5:20 or resid 22:24 or resid...
61(chain F and (resid 5:20 or resid 22:24 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5:20 or resid 22:24 or resid...A5 - 20
121(chain A and (resid 5:20 or resid 22:24 or resid...A22 - 24
131(chain A and (resid 5:20 or resid 22:24 or resid...A26 - 31
141(chain A and (resid 5:20 or resid 22:24 or resid...A58 - 67
151(chain A and (resid 5:20 or resid 22:24 or resid...A2 - 56
161(chain A and (resid 5:20 or resid 22:24 or resid...A69 - 73
171(chain A and (resid 5:20 or resid 22:24 or resid...A2 - 97
181(chain A and (resid 5:20 or resid 22:24 or resid...A99 - 112
191(chain A and (resid 5:20 or resid 22:24 or resid...A0
1101(chain A and (resid 5:20 or resid 22:24 or resid...A143 - 14
1111(chain A and (resid 5:20 or resid 22:24 or resid...A147 - 159
1121(chain A and (resid 5:20 or resid 22:24 or resid...A162 - 165
1131(chain A and (resid 5:20 or resid 22:24 or resid...A233
1141(chain A and (resid 5:20 or resid 22:24 or resid...A2 - 298
1151(chain A and (resid 5:20 or resid 22:24 or resid...A268 - 279
1161(chain A and (resid 5:20 or resid 22:24 or resid...A2 - 298
1171(chain A and (resid 5:20 or resid 22:24 or resid...A289 - 29
1181(chain A and (resid 5:20 or resid 22:24 or resid...A21
1191(chain A and (resid 5:20 or resid 22:24 or resid...A293
1201(chain A and (resid 5:20 or resid 22:24 or resid...A295 - 298
211(chain B and (resid 5:20 or resid 22:24 or resid...B5 - 20
221(chain B and (resid 5:20 or resid 22:24 or resid...B22 - 24
231(chain B and (resid 5:20 or resid 22:24 or resid...B26 - 31
241(chain B and (resid 5:20 or resid 22:24 or resid...B58 - 67
251(chain B and (resid 5:20 or resid 22:24 or resid...B-7 - 56
261(chain B and (resid 5:20 or resid 22:24 or resid...B69 - 73
271(chain B and (resid 5:20 or resid 22:24 or resid...B-7 - 97
281(chain B and (resid 5:20 or resid 22:24 or resid...B99 - 112
291(chain B and (resid 5:20 or resid 22:24 or resid...B0
2101(chain B and (resid 5:20 or resid 22:24 or resid...B143 - 14
2111(chain B and (resid 5:20 or resid 22:24 or resid...B147 - 159
2121(chain B and (resid 5:20 or resid 22:24 or resid...B162 - 165
2131(chain B and (resid 5:20 or resid 22:24 or resid...B233
2141(chain B and (resid 5:20 or resid 22:24 or resid...B-7 - 298
2151(chain B and (resid 5:20 or resid 22:24 or resid...B268 - 279
2161(chain B and (resid 5:20 or resid 22:24 or resid...B-7 - 298
2171(chain B and (resid 5:20 or resid 22:24 or resid...B289 - 29
2181(chain B and (resid 5:20 or resid 22:24 or resid...B21
2191(chain B and (resid 5:20 or resid 22:24 or resid...B293
2201(chain B and (resid 5:20 or resid 22:24 or resid...B295 - 298
311(chain C and (resid 5:20 or resid 22:24 or resid...C5 - 20
321(chain C and (resid 5:20 or resid 22:24 or resid...C22 - 24
331(chain C and (resid 5:20 or resid 22:24 or resid...C26 - 31
341(chain C and (resid 5:20 or resid 22:24 or resid...C58 - 67
351(chain C and (resid 5:20 or resid 22:24 or resid...C4 - 56
361(chain C and (resid 5:20 or resid 22:24 or resid...C69 - 73
371(chain C and (resid 5:20 or resid 22:24 or resid...C4 - 97
381(chain C and (resid 5:20 or resid 22:24 or resid...C99 - 112
391(chain C and (resid 5:20 or resid 22:24 or resid...C0
3101(chain C and (resid 5:20 or resid 22:24 or resid...C143 - 14
3111(chain C and (resid 5:20 or resid 22:24 or resid...C147 - 159
3121(chain C and (resid 5:20 or resid 22:24 or resid...C162 - 165
3131(chain C and (resid 5:20 or resid 22:24 or resid...C233
3141(chain C and (resid 5:20 or resid 22:24 or resid...C4 - 298
3151(chain C and (resid 5:20 or resid 22:24 or resid...C268 - 279
3161(chain C and (resid 5:20 or resid 22:24 or resid...C4 - 298
3171(chain C and (resid 5:20 or resid 22:24 or resid...C289 - 29
3181(chain C and (resid 5:20 or resid 22:24 or resid...C21
3191(chain C and (resid 5:20 or resid 22:24 or resid...C293
3201(chain C and (resid 5:20 or resid 22:24 or resid...C295 - 298
411(chain D and (resid 5:20 or resid 22:24 or resid...D5 - 20
421(chain D and (resid 5:20 or resid 22:24 or resid...D22 - 24
431(chain D and (resid 5:20 or resid 22:24 or resid...D26 - 31
441(chain D and (resid 5:20 or resid 22:24 or resid...D58 - 67
451(chain D and (resid 5:20 or resid 22:24 or resid...D-7 - 56
461(chain D and (resid 5:20 or resid 22:24 or resid...D69 - 73
471(chain D and (resid 5:20 or resid 22:24 or resid...D-7 - 97
481(chain D and (resid 5:20 or resid 22:24 or resid...D99 - 112
491(chain D and (resid 5:20 or resid 22:24 or resid...D0
4101(chain D and (resid 5:20 or resid 22:24 or resid...D143 - 14
4111(chain D and (resid 5:20 or resid 22:24 or resid...D147 - 159
4121(chain D and (resid 5:20 or resid 22:24 or resid...D162 - 165
4131(chain D and (resid 5:20 or resid 22:24 or resid...D233
4141(chain D and (resid 5:20 or resid 22:24 or resid...D-7 - 298
4151(chain D and (resid 5:20 or resid 22:24 or resid...D268 - 279
4161(chain D and (resid 5:20 or resid 22:24 or resid...D-7 - 298
4171(chain D and (resid 5:20 or resid 22:24 or resid...D289 - 29
4181(chain D and (resid 5:20 or resid 22:24 or resid...D21
4191(chain D and (resid 5:20 or resid 22:24 or resid...D293
4201(chain D and (resid 5:20 or resid 22:24 or resid...D295 - 298
511(chain E and (resid 5:20 or resid 22:24 or resid...E5 - 20
521(chain E and (resid 5:20 or resid 22:24 or resid...E22 - 24
531(chain E and (resid 5:20 or resid 22:24 or resid...E26 - 31
541(chain E and (resid 5:20 or resid 22:24 or resid...E58 - 67
551(chain E and (resid 5:20 or resid 22:24 or resid...E3 - 56
561(chain E and (resid 5:20 or resid 22:24 or resid...E69 - 73
571(chain E and (resid 5:20 or resid 22:24 or resid...E3 - 97
581(chain E and (resid 5:20 or resid 22:24 or resid...E99 - 112
591(chain E and (resid 5:20 or resid 22:24 or resid...E0
5101(chain E and (resid 5:20 or resid 22:24 or resid...E143 - 14
5111(chain E and (resid 5:20 or resid 22:24 or resid...E147 - 159
5121(chain E and (resid 5:20 or resid 22:24 or resid...E162 - 165
5131(chain E and (resid 5:20 or resid 22:24 or resid...E233
5141(chain E and (resid 5:20 or resid 22:24 or resid...E3 - 298
5151(chain E and (resid 5:20 or resid 22:24 or resid...E268 - 279
5161(chain E and (resid 5:20 or resid 22:24 or resid...E3 - 298
5171(chain E and (resid 5:20 or resid 22:24 or resid...E289 - 29
5181(chain E and (resid 5:20 or resid 22:24 or resid...E21
5191(chain E and (resid 5:20 or resid 22:24 or resid...E293
5201(chain E and (resid 5:20 or resid 22:24 or resid...E295 - 298
611(chain F and (resid 5:20 or resid 22:24 or resid...F5 - 20
621(chain F and (resid 5:20 or resid 22:24 or resid...F22 - 24
631(chain F and (resid 5:20 or resid 22:24 or resid...F26 - 31
641(chain F and (resid 5:20 or resid 22:24 or resid...F58 - 67
651(chain F and (resid 5:20 or resid 22:24 or resid...F3 - 56
661(chain F and (resid 5:20 or resid 22:24 or resid...F69 - 73
671(chain F and (resid 5:20 or resid 22:24 or resid...F3 - 97
681(chain F and (resid 5:20 or resid 22:24 or resid...F99 - 112
691(chain F and (resid 5:20 or resid 22:24 or resid...F0
6101(chain F and (resid 5:20 or resid 22:24 or resid...F143 - 14
6111(chain F and (resid 5:20 or resid 22:24 or resid...F147 - 159
6121(chain F and (resid 5:20 or resid 22:24 or resid...F162 - 165
6131(chain F and (resid 5:20 or resid 22:24 or resid...F233
6141(chain F and (resid 5:20 or resid 22:24 or resid...F3 - 298
6151(chain F and (resid 5:20 or resid 22:24 or resid...F268 - 279
6161(chain F and (resid 5:20 or resid 22:24 or resid...F3 - 298
6171(chain F and (resid 5:20 or resid 22:24 or resid...F289 - 29
6181(chain F and (resid 5:20 or resid 22:24 or resid...F21
6191(chain F and (resid 5:20 or resid 22:24 or resid...F293
6201(chain F and (resid 5:20 or resid 22:24 or resid...F295 - 298

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


Mass: 34186.246 Da / Num. of mol.: 6 / Mutation: N84D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: dapA, Cj0806 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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Non-polymers , 10 types, 2255 molecules

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


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2199 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 288.15 K / Method: microbatch / pH: 7.4
Details: 0.7 M Magnesium acetate, 10 % PEG8000, 0.1 M Sodium acetate (pH 7.4), 120 mML-Lysine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→45.883 Å / Num. obs: 233653 / % possible obs: 98.8 % / Redundancy: 15 % / Biso Wilson estimate: 12.17 Å2 / CC1/2: 0.99 / Net I/σ(I): 20.49
Reflection shellResolution: 1.64→1.699 Å / Rmerge(I) obs: 0.1897 / Num. unique obs: 22156 / % possible all: 94.35

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2398refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LY8

4ly8


Resolution: 1.64→45.883 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.169 11682 5 %
Rwork0.1375 221957 -
obs0.1391 233639 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.94 Å2 / Biso mean: 15.2207 Å2 / Biso min: 1.84 Å2
Refinement stepCycle: final / Resolution: 1.64→45.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13851 0 202 2199 16252
Biso mean--34.61 26.4 -
Num. residues----1802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214355
X-RAY DIFFRACTIONf_angle_d1.19919319
X-RAY DIFFRACTIONf_chiral_restr0.0772206
X-RAY DIFFRACTIONf_plane_restr0.0082466
X-RAY DIFFRACTIONf_dihedral_angle_d14.9698790
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7246X-RAY DIFFRACTION5.369TORSIONAL
12B7246X-RAY DIFFRACTION5.369TORSIONAL
13C7246X-RAY DIFFRACTION5.369TORSIONAL
14D7246X-RAY DIFFRACTION5.369TORSIONAL
15E7246X-RAY DIFFRACTION5.369TORSIONAL
16F7246X-RAY DIFFRACTION5.369TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.64-1.65870.20423450.1548655688
1.6587-1.67820.19313760.1509713896
1.6782-1.69860.16773870.1326735399
1.6986-1.72010.16973880.1346737699
1.7201-1.74280.18693890.137738299
1.7428-1.76670.16963890.13157391100
1.7667-1.79190.17533900.1276741699
1.7919-1.81860.17183910.133743399
1.8186-1.84710.1743860.1348734399
1.8471-1.87730.18123880.1384736999
1.8773-1.90970.17563810.1368722797
1.9097-1.94440.18213890.1355739399
1.9444-1.98180.18083900.14127411100
1.9818-2.02230.18063900.13657411100
2.0223-2.06630.16543910.13627431100
2.0663-2.11430.1823900.1384740199
2.1143-2.16720.17183910.13457442100
2.1672-2.22580.17723910.13697431100
2.2258-2.29130.17583850.1381731098
2.2913-2.36520.17053920.1371745199
2.3652-2.44980.17633930.14327469100
2.4498-2.54790.16913930.14037457100
2.5479-2.66380.16783940.13397495100
2.6638-2.80420.16973930.137745899
2.8042-2.97990.17863900.1465740399
2.9799-3.20990.15643950.1437751499
3.2099-3.53280.17563950.1447750899
3.5328-4.04380.16543980.1302755899
4.0438-5.09370.1353990.1204758999
5.0937-7.330.15774130.14847841100

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