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- PDB-9frt: Crystal structure of trans-o-hydroxybenzylidenepyruvate hydratase... -

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Basic information

Entry
Database: PDB / ID: 9frt
TitleCrystal structure of trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3
ComponentsTrans-O-hydroxybenzylidenepyruvate hydratase-aldolase
KeywordsLYASE / hydratase / aldolase
Function / homology
Function and homology information


trans-o-hydroxybenzylidenepyruvate hydratase-aldolase / 4-hydroxy-tetrahydrodipicolinate synthase activity / catabolic process
Similarity search - Function
: / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMilani, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural snapshots of the aldol condensation reaction of the enzyme trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from Pseudomonas fluorescens N3.
Authors: Ferrara, S. / Braggiotti, B. / Mastrangelo, E. / Di Gennaro, P. / Bertoni, G. / Milani, M.
History
DepositionJun 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
C: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
D: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
G: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
H: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
J: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
K: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,35832
Polymers307,1028
Non-polymers2,25624
Water57,2883180
1
A: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
B: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
C: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
D: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,67916
Polymers153,5514
Non-polymers1,12812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
H: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
J: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
K: Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,67916
Polymers153,5514
Non-polymers1,12812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.700, 199.890, 144.150
Angle α, β, γ (deg.)90.000, 133.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A
137A
147A
158A
168A
179A
189A
1910A
2010A
2111A
2211A
2312A
2412A
2513A
2613A
2714A
2814A
2915A
3015A
3116A
3216A
3317A
3417A
3518A
3618A
3719A
3819A
3920A
4020A
4121A
4221A
4322A
4422A
4523A
4623A
4724A
4824A
4925A
5025A
5126A
5226A
5327A
5427A
5528A
5628A

NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111SERSERLEULEU9 - 33321 - 345
211SERSERLEULEU9 - 33321 - 345
322THRTHRLYSLYS8 - 33420 - 346
422THRTHRLYSLYS8 - 33420 - 346
533THRTHRGLUGLU8 - 33220 - 344
633THRTHRGLUGLU8 - 33220 - 344
744SERSERLEULEU9 - 33321 - 345
844SERSERLEULEU9 - 33321 - 345
955THRTHRLYSLYS8 - 33420 - 346
1055THRTHRLYSLYS8 - 33420 - 346
1166SERSERGLUGLU9 - 33221 - 344
1266SERSERGLUGLU9 - 33221 - 344
1377SERSERLEULEU9 - 33321 - 345
1477SERSERLEULEU9 - 33321 - 345
1588SERSERLEULEU9 - 33321 - 345
1688SERSERLEULEU9 - 33321 - 345
1799SERSERGLUGLU9 - 33221 - 344
1899SERSERGLUGLU9 - 33221 - 344
191010SERSERLYSLYS9 - 33421 - 346
201010SERSERLYSLYS9 - 33421 - 346
211111SERSERLEULEU9 - 33321 - 345
221111SERSERLEULEU9 - 33321 - 345
231212SERSERGLUGLU9 - 33221 - 344
241212SERSERGLUGLU9 - 33221 - 344
251313SERSERLYSLYS9 - 33421 - 346
261313SERSERLYSLYS9 - 33421 - 346
271414THRTHRGLUGLU8 - 33220 - 344
281414THRTHRGLUGLU8 - 33220 - 344
291515SERSERLEULEU9 - 33321 - 345
301515SERSERLEULEU9 - 33321 - 345
311616THRTHRLYSLYS8 - 33420 - 346
321616THRTHRLYSLYS8 - 33420 - 346
331717SERSERGLUGLU9 - 33221 - 344
341717SERSERGLUGLU9 - 33221 - 344
351818SERSERLEULEU9 - 33321 - 345
361818SERSERLEULEU9 - 33321 - 345
371919SERSERGLUGLU9 - 33221 - 344
381919SERSERGLUGLU9 - 33221 - 344
392020THRTHRGLUGLU8 - 33220 - 344
402020THRTHRGLUGLU8 - 33220 - 344
412121SERSERGLUGLU9 - 33221 - 344
422121SERSERGLUGLU9 - 33221 - 344
432222SERSERGLUGLU9 - 33221 - 344
442222SERSERGLUGLU9 - 33221 - 344
452323SERSERLEULEU9 - 33321 - 345
462323SERSERLEULEU9 - 33321 - 345
472424SERSERGLUGLU9 - 33221 - 344
482424SERSERGLUGLU9 - 33221 - 344
492525SERSERLYSLYS9 - 33421 - 346
502525SERSERLYSLYS9 - 33421 - 346
512626SERSERGLUGLU9 - 33221 - 344
522626SERSERGLUGLU9 - 33221 - 344
532727SERSERLEULEU9 - 33321 - 345
542727SERSERLEULEU9 - 33321 - 345
552828SERSERGLUGLU9 - 33221 - 344
562828SERSERGLUGLU9 - 33221 - 344

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56

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Components

#1: Protein
Trans-O-hydroxybenzylidenepyruvate hydratase-aldolase / 2'-hydroxybenzalpyruvate aldolase


Mass: 38387.730 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nahE / Production host: Escherichia coli (E. coli)
References: UniProt: C3KFM9, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.503
pseudo-merohedral22H, -K, -H-L20.0429
pseudo-merohedral33-K, -H, -1/2H+1/2K-L30.3341
pseudo-merohedral44K, H, -1/2H-1/2K-L40.12
ReflectionResolution: 1.96→36.04 Å / Num. obs: 277447 / % possible obs: 95.6 % / Redundancy: 2 % / CC1/2: 0.933 / Rrim(I) all: 0.134 / Net I/σ(I): 5.1
Reflection shellResolution: 1.96→2.06 Å / Mean I/σ(I) obs: 3.4 / Num. unique obs: 40163 / CC1/2: 0.897 / Rrim(I) all: 0.218

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→36.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1684 13909 5.02 %
Rwork0.1394 263188 -
all0.141 --
obs-277097 94.739 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1-3.704 Å20 Å2-0.56 Å2
2--4.342 Å20 Å2
3----8.046 Å2
Refinement stepCycle: LAST / Resolution: 1.96→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20265 0 128 3180 23573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01221097
X-RAY DIFFRACTIONr_bond_other_d0.0020.01619825
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.81628765
X-RAY DIFFRACTIONr_angle_other_deg0.9831.75745679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38852674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.425172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.272103403
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.54910910
X-RAY DIFFRACTIONr_chiral_restr0.1010.23184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0225257
X-RAY DIFFRACTIONr_gen_planes_other0.0140.024867
X-RAY DIFFRACTIONr_nbd_refined0.2350.24808
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.219618
X-RAY DIFFRACTIONr_nbtor_refined0.1830.210634
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.210607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.22621
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1510.218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3830.246
X-RAY DIFFRACTIONr_nbd_other0.2390.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2920.240
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1330.24
X-RAY DIFFRACTIONr_mcbond_it2.0721.53210507
X-RAY DIFFRACTIONr_mcbond_other2.0651.53210507
X-RAY DIFFRACTIONr_mcangle_it2.9212.74313139
X-RAY DIFFRACTIONr_mcangle_other2.9212.74313140
X-RAY DIFFRACTIONr_scbond_it2.8391.81210590
X-RAY DIFFRACTIONr_scbond_other2.8071.80410527
X-RAY DIFFRACTIONr_scangle_it4.1823.19915591
X-RAY DIFFRACTIONr_scangle_other4.1383.18215496
X-RAY DIFFRACTIONr_lrange_it6.21716.49426168
X-RAY DIFFRACTIONr_lrange_other5.89815.87125048
X-RAY DIFFRACTIONr_ncsr_local_group_10.0620.0511089
X-RAY DIFFRACTIONr_ncsr_local_group_20.0550.0511248
X-RAY DIFFRACTIONr_ncsr_local_group_30.060.0511120
X-RAY DIFFRACTIONr_ncsr_local_group_40.0560.0511201
X-RAY DIFFRACTIONr_ncsr_local_group_50.0630.0511190
X-RAY DIFFRACTIONr_ncsr_local_group_60.0630.0511067
X-RAY DIFFRACTIONr_ncsr_local_group_70.0630.0511145
X-RAY DIFFRACTIONr_ncsr_local_group_80.0630.0511121
X-RAY DIFFRACTIONr_ncsr_local_group_90.0570.0511113
X-RAY DIFFRACTIONr_ncsr_local_group_100.0560.0511141
X-RAY DIFFRACTIONr_ncsr_local_group_110.060.0511125
X-RAY DIFFRACTIONr_ncsr_local_group_120.0630.0511060
X-RAY DIFFRACTIONr_ncsr_local_group_130.060.0511177
X-RAY DIFFRACTIONr_ncsr_local_group_140.0620.0511212
X-RAY DIFFRACTIONr_ncsr_local_group_150.0610.0511265
X-RAY DIFFRACTIONr_ncsr_local_group_160.0620.0511257
X-RAY DIFFRACTIONr_ncsr_local_group_170.0660.0511137
X-RAY DIFFRACTIONr_ncsr_local_group_180.0630.0511206
X-RAY DIFFRACTIONr_ncsr_local_group_190.0560.0511101
X-RAY DIFFRACTIONr_ncsr_local_group_200.0540.0511156
X-RAY DIFFRACTIONr_ncsr_local_group_210.0620.0511024
X-RAY DIFFRACTIONr_ncsr_local_group_220.0620.0511060
X-RAY DIFFRACTIONr_ncsr_local_group_230.0590.0511202
X-RAY DIFFRACTIONr_ncsr_local_group_240.0670.0511108
X-RAY DIFFRACTIONr_ncsr_local_group_250.0610.0511218
X-RAY DIFFRACTIONr_ncsr_local_group_260.0560.0511053
X-RAY DIFFRACTIONr_ncsr_local_group_270.0540.0511105
X-RAY DIFFRACTIONr_ncsr_local_group_280.0590.0511179
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.061840.05009
12AX-RAY DIFFRACTIONLocal ncs0.061840.05009
23AX-RAY DIFFRACTIONLocal ncs0.055420.05009
24AX-RAY DIFFRACTIONLocal ncs0.055420.05009
35AX-RAY DIFFRACTIONLocal ncs0.060340.05009
36AX-RAY DIFFRACTIONLocal ncs0.060340.05009
47AX-RAY DIFFRACTIONLocal ncs0.056410.05009
48AX-RAY DIFFRACTIONLocal ncs0.056410.05009
59AX-RAY DIFFRACTIONLocal ncs0.062670.05009
510AX-RAY DIFFRACTIONLocal ncs0.062670.05009
611AX-RAY DIFFRACTIONLocal ncs0.062950.05009
612AX-RAY DIFFRACTIONLocal ncs0.062950.05009
713AX-RAY DIFFRACTIONLocal ncs0.062760.05009
714AX-RAY DIFFRACTIONLocal ncs0.062760.05009
815AX-RAY DIFFRACTIONLocal ncs0.062760.05009
816AX-RAY DIFFRACTIONLocal ncs0.062760.05009
917AX-RAY DIFFRACTIONLocal ncs0.05690.0501
918AX-RAY DIFFRACTIONLocal ncs0.05690.0501
1019AX-RAY DIFFRACTIONLocal ncs0.05620.05009
1020AX-RAY DIFFRACTIONLocal ncs0.05620.05009
1121AX-RAY DIFFRACTIONLocal ncs0.060050.05009
1122AX-RAY DIFFRACTIONLocal ncs0.060050.05009
1223AX-RAY DIFFRACTIONLocal ncs0.063250.05009
1224AX-RAY DIFFRACTIONLocal ncs0.063250.05009
1325AX-RAY DIFFRACTIONLocal ncs0.060210.05009
1326AX-RAY DIFFRACTIONLocal ncs0.060210.05009
1427AX-RAY DIFFRACTIONLocal ncs0.062250.0501
1428AX-RAY DIFFRACTIONLocal ncs0.062250.0501
1529AX-RAY DIFFRACTIONLocal ncs0.060540.05009
1530AX-RAY DIFFRACTIONLocal ncs0.060540.05009
1631AX-RAY DIFFRACTIONLocal ncs0.061810.05009
1632AX-RAY DIFFRACTIONLocal ncs0.061810.05009
1733AX-RAY DIFFRACTIONLocal ncs0.066150.0501
1734AX-RAY DIFFRACTIONLocal ncs0.066150.0501
1835AX-RAY DIFFRACTIONLocal ncs0.063320.05009
1836AX-RAY DIFFRACTIONLocal ncs0.063320.05009
1937AX-RAY DIFFRACTIONLocal ncs0.055570.05009
1938AX-RAY DIFFRACTIONLocal ncs0.055570.05009
2039AX-RAY DIFFRACTIONLocal ncs0.053820.0501
2040AX-RAY DIFFRACTIONLocal ncs0.053820.0501
2141AX-RAY DIFFRACTIONLocal ncs0.062480.05009
2142AX-RAY DIFFRACTIONLocal ncs0.062480.05009
2243AX-RAY DIFFRACTIONLocal ncs0.062310.05009
2244AX-RAY DIFFRACTIONLocal ncs0.062310.05009
2345AX-RAY DIFFRACTIONLocal ncs0.058580.0501
2346AX-RAY DIFFRACTIONLocal ncs0.058580.0501
2447AX-RAY DIFFRACTIONLocal ncs0.067350.05009
2448AX-RAY DIFFRACTIONLocal ncs0.067350.05009
2549AX-RAY DIFFRACTIONLocal ncs0.06110.0501
2550AX-RAY DIFFRACTIONLocal ncs0.06110.0501
2651AX-RAY DIFFRACTIONLocal ncs0.055790.05009
2652AX-RAY DIFFRACTIONLocal ncs0.055790.05009
2753AX-RAY DIFFRACTIONLocal ncs0.054260.05009
2754AX-RAY DIFFRACTIONLocal ncs0.054260.05009
2855AX-RAY DIFFRACTIONLocal ncs0.059220.0501
2856AX-RAY DIFFRACTIONLocal ncs0.059220.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0070.1899850.15217703X-RAY DIFFRACTION86.6027
2.007-2.0620.17110770.13719532X-RAY DIFFRACTION97.6545
2.062-2.1220.17610410.13418862X-RAY DIFFRACTION97.2871
2.122-2.1880.1818870.13318413X-RAY DIFFRACTION97.0044
2.188-2.2590.1679710.12517748X-RAY DIFFRACTION97.2365
2.259-2.3390.1689100.12917081X-RAY DIFFRACTION96.757
2.339-2.4270.1799180.12916466X-RAY DIFFRACTION96.6422
2.427-2.5260.1626750.12616084X-RAY DIFFRACTION96.377
2.526-2.6380.1747390.13215135X-RAY DIFFRACTION96.0315
2.638-2.7670.1897450.1314560X-RAY DIFFRACTION96.0344
2.767-2.9160.1516460.13313690X-RAY DIFFRACTION95.3953
2.916-3.0930.166700.13912990X-RAY DIFFRACTION95.1187
3.093-3.3070.1767030.14312000X-RAY DIFFRACTION94.6149
3.307-3.5710.1626520.15811146X-RAY DIFFRACTION94.0304
3.571-3.9120.1734760.15210295X-RAY DIFFRACTION93.2958
3.912-4.3730.1515490.1359093X-RAY DIFFRACTION92.6492
4.373-5.0480.1534520.1367991X-RAY DIFFRACTION91.5429
5.048-6.180.1623670.1666648X-RAY DIFFRACTION90.2831
6.18-8.7270.1542900.1575085X-RAY DIFFRACTION88.6379
8.727-36.040.2091560.172666X-RAY DIFFRACTION83.2694

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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

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