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- PDB-7rf9: O2-, PLP-dependent desaturase Plu4 intermediate-bound enzyme -

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Basic information

Entry
Database: PDB / ID: 7rf9
TitleO2-, PLP-dependent desaturase Plu4 intermediate-bound enzyme
ComponentsAminotran_1_2 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / arginine desaturase / oxygen- and PLP-dependent oxidase / Fold Type I / biosynthesis
Function / homology
Function and homology information


biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ACETATE ION / 2-(2-ETHOXYETHOXY)ETHANOL / Chem-EJ1 / Aminotransferase class I/classII domain-containing protein
Similarity search - Component
Biological speciesPseudoalteromonas luteoviolacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.926 Å
AuthorsHoffarth, E.R. / Ryan, K.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-03778 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases.
Authors: Hoffarth, E.R. / Caddell Haatveit, K. / Kuatsjah, E. / MacNeil, G.A. / Saroya, S. / Walsby, C.J. / Eltis, L.D. / Houk, K.N. / Garcia-Borras, M. / Ryan, K.S.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotran_1_2 domain-containing protein
B: Aminotran_1_2 domain-containing protein
C: Aminotran_1_2 domain-containing protein
D: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,91739
Polymers178,5574
Non-polymers4,36035
Water20,3571130
1
A: Aminotran_1_2 domain-containing protein
B: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,54120
Polymers89,2782
Non-polymers2,26218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-25 kcal/mol
Surface area26530 Å2
MethodPISA
2
C: Aminotran_1_2 domain-containing protein
D: Aminotran_1_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,37619
Polymers89,2782
Non-polymers2,09817
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-25 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.922, 70.279, 138.568
Angle α, β, γ (deg.)90.000, 98.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aminotran_1_2 domain-containing protein


Mass: 44639.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas luteoviolacea (bacteria)
Gene: JF50_03865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C1MLE8

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Non-polymers , 7 types, 1165 molecules

#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.: 5 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EJ1 / (2E)-5-carbamimidamido-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pentanoic acid


Mass: 403.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1130 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris:HCl; 27% PEG 3350; 0.2 M ammonium acetate; microseeded from crystals grown at pH 6.0; soaked with 2 mM PLP and 3 mM L-arginine for 8 min
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.926→39.16 Å / Num. obs: 106646 / % possible obs: 98.8 % / Redundancy: 13.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.054 / Rrim(I) all: 0.199 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.93-1.9612.32.2115893148010.8520.6462.3071.990.7
10.55-39.1614.10.09699437060.9960.0260.0992998.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C3D
Resolution: 1.926→38.328 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 5353 5.02 %
Rwork0.1509 101185 -
obs0.1532 106538 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.75 Å2 / Biso mean: 30.4988 Å2 / Biso min: 12.95 Å2
Refinement stepCycle: final / Resolution: 1.926→38.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11975 0 289 1130 13394
Biso mean--41.17 39.35 -
Num. residues----1513
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9263-1.94820.33061420.2704291986
1.9482-1.97110.27971690.22543412100
1.9711-1.99520.26431670.2125334799
1.9952-2.02040.26881650.2095338599
2.0204-2.0470.27281750.1994333399
2.047-2.07510.25181720.1909332197
2.0751-2.10470.23591850.17873377100
2.1047-2.13610.24071920.16923407100
2.1361-2.16950.22561850.17373330100
2.1695-2.20510.24211720.16723438100
2.2051-2.24310.24461560.16813412100
2.2431-2.28390.22441900.1707338199
2.2839-2.32780.23471700.16023344100
2.3278-2.37530.20731650.1585341799
2.3753-2.42690.21841880.159340599
2.4269-2.48340.23651700.1569331598
2.4834-2.54550.23091620.1574336598
2.5455-2.61430.21262100.15213365100
2.6143-2.69120.20322050.14193414100
2.6912-2.7780.2071810.1426339999
2.778-2.87730.20432000.14833358100
2.8773-2.99240.20951820.15153381100
2.9924-3.12860.19371720.1467341899
3.1286-3.29340.19811770.1477333798
3.2934-3.49960.17311750.13813416100
3.4996-3.76960.16871720.1283440100
3.7696-4.14860.12982100.11483411100
4.1486-4.74790.14681720.1173339898
4.7479-5.97820.16391770.1491345399
5.9782-38.3280.17921950.1607348798
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3559-0.75210.32474.52071.74852.2721-0.0042-0.22860.09030.2686-0.1410.0739-0.0449-0.02970.0060.2323-0.0089-0.0180.1981-0.01220.163427.414939.4962100.8092
20.8131-0.1665-00.9890.17870.94-0.05070.10450.1324-0.0547-0.02990.1208-0.2983-0.1063-0.03230.33670.0393-0.02670.20090.03430.250920.218450.331677.7068
31.45070.22240.22161.7619-0.161.06580.01610.11-0.1344-0.0824-0.0491-0.30430.08410.1913-0.00770.17770.02520.01340.1580.01450.191938.60528.185481.9811
42.0256-0.7163-0.91984.64091.3682.79740.11760.20190.0925-0.2328-0.0702-0.5005-0.20380.255-0.13340.19240.00780.02020.25870.05110.220344.404235.53678.341
52.7778-1.8459-1.40973.07681.92412.28520.01210.15390.0804-0.0979-0.0671-0.0711-0.07540.0622-0.13110.16320.0119-0.00770.15030.02490.153632.720938.314478.5332
60.6519-0.02530.41320.93490.49261.5676-0.0546-0.05980.0610.1942-0.0008-0.1269-0.03610.11440.02470.2309-0.0062-0.02050.15630.02570.180635.411738.800295.5925
75.0646-3.14922.98396.6011-3.94525.4513-0.0979-0.603-0.30050.8990.14340.0572-0.00350.1746-0.37050.5387-0.0111-0.01540.32750.02310.259236.475743.3262115.4844
81.539-0.97280.25995.4686-0.70341.16-0.09170.09770.1362-0.27550.1099-0.1129-0.0316-0.17960.1170.24870.0013-0.08080.3303-0.02760.21778.15335.958470.255
91.1670.87110.30042.00810.16611.54950.01580.08820.11450.0273-0.07040.1296-0.2509-0.2625-0.03740.24870.04820.02780.2282-0.03330.23288.712643.962296.6025
101.20990.051-0.03481.29440.60291.45450.0109-0.0293-0.16750.1562-0.03230.01430.2201-0.071-0.05130.2217-0.03040.00430.1729-0.01550.214612.400820.47187.6663
112.0468-0.88510.52241.4673-0.6070.5280.0364-0.0221-0.4196-0.12920.0390.35420.3223-0.3409-0.02560.2671-0.07890.02780.2856-0.04790.3154-0.000612.591383.0133
121.69650.72770.08545.4342-1.02722.49380.0222-0.1542-0.22120.5719-0.05610.32790.2521-0.5275-0.10440.2562-0.06150.05480.2586-0.05230.2445-1.481818.220590.805
131.33720.15240.41354.7301-0.43780.82020.0947-0.0538-0.05520.0789-0.20370.17650.1389-0.1564-0.11720.1752-0.01380.02680.207-0.04660.16995.775327.405792.2642
141.9658-1.29010.45552.90780.07961.012-0.0028-0.09710.03110.1366-0.05490.0994-0.0429-0.149-0.06450.1959-0.00130.02390.1673-0.02150.110712.607933.506594.5732
151.636-0.6728-0.26350.84461.51815.3887-0.1318-0.05680.2578-0.199-0.32790.3954-0.6607-1.25930.03110.26040.1068-0.02580.4715-0.07620.3828-8.999238.16676.0447
161.55760.119-0.06691.7592-0.15822.25810.02410.3252-0.1516-0.2926-0.15150.25430.0359-0.4927-0.06990.25230.0331-0.0740.4196-0.10860.2967-3.274527.148864.0326
171.7857-2.25110.96577.3304-2.76093.2152-0.02330.24110.0616-0.3103-0.1434-0.25940.0584-0.17980.11710.1934-0.0188-0.00720.2916-0.05360.2153.575324.683967.4507
181.72290.30530.79077.93354.04886.1502-0.16590.16460.1684-0.789-0.14710.2553-0.9968-0.67940.25860.3950.1098-0.09130.3820.01880.2905-3.702737.925258.7609
192.03730.30230.19823.3951-1.46342.279-0.02950.17580.0581-0.11980.0224-0.1199-0.02890.00480.01130.21090.0301-0.01850.17680.0120.158854.830173.9098105.9596
200.49140.2682-0.10530.1295-0.13920.76030.0426-0.17780.27830.1366-0.0361-0.024-0.21860.0765-0.0680.3499-0.0183-0.00430.238-0.04850.280864.355984.5451128.0748
211.79480.2277-0.4194.15170.54932.0348-0.0366-0.28820.11560.30890.0753-0.0555-0.08030.0223-0.01510.14640.0355-0.0250.1882-0.02020.13654.548667.6468131.3091
222.1812-0.8689-0.16821.25630.05941.0211-0.0073-0.1376-0.2972-0.00280.03840.2830.05-0.08540.04770.2093-0.017-0.0170.16470.00740.215440.63460.7799123.1157
232.12050.1145-0.12370.9262-0.38351.0639-0.0532-0.26270.02390.04530.07770.0928-0.0752-0.08110.04460.22790.0230.00220.1876-0.01940.165345.891371.5731129.2293
241.27830.16390.11192.0925-0.98890.6263-0.0952-0.14520.07390.32050.0589-0.0534-0.32130.02350.10710.2714-0.00110.00230.1889-0.04090.115760.674373.1701129.6707
250.82881.17080.77155.17253.24173.1442-0.1999-0.11020.11140.01980.1580.1955-0.6687-0.29650.27960.39770.06470.0120.21460.03740.309843.672186.3264109.7979
261.9145-0.09010.14191.90380.30152.3210.0680.2543-0.0591-0.2764-0.05790.26630.1076-0.24950.0520.2930.0164-0.07980.2040.00810.199639.488772.2146101.4505
271.39221.8245-1.04915.2222-2.51052.2571-0.04970.1165-0.0143-0.2702-0.0193-0.00470.1548-0.0871-0.00680.1820.0205-0.050.1583-0.00880.173443.512166.5117105.855
284.43073.13081.83787.51272.40383.7945-0.02850.57430.3245-0.559-0.04440.1709-0.1634-0.0044-0.08340.3580.0720.00140.29180.06120.192946.088780.272594.5982
290.87811.13590.91946.6433-0.71371.5453-0.0964-0.15870.17140.5480.1392-0.1013-0.2495-0.24550.10190.26140.0586-0.03280.2877-0.05170.233877.367870.2451133.437
300.9685-1.190.47562.02850.06450.9217-0.01070.11620.2952-0.17760.0072-0.2642-0.24510.19060.0730.2865-0.03460.03490.21020.02330.236173.674877.3172108.3996
311.4110.638-0.22692.36720.00440.41940.0190.11850.0494-0.1420.0211-0.00290.01980.0141-0.04330.22370.0259-0.00990.19470.01010.157870.495458.075111.5525
321.8173-0.14581.08990.6891-0.13061.6213-0.004-0.1258-0.2225-0.00550.04050.02050.0716-0.0971-0.03880.21140.01660.00230.17220.03910.205669.539548.8388124.9014
331.85530.66630.31961.31340.3740.2101-0.052-0.02-0.28190.04560.0723-0.12030.2040.16280.0390.27670.0458-0.00180.2190.01520.229282.398845.1394121.3807
341.6382-0.4207-0.22195.13191.19481.1984-0.01810.0944-0.0931-0.22650.0036-0.25540.06240.2056-0.02620.20250.034-0.00010.18420.0180.123483.511750.8256113.2681
351.7346-1.0185-0.09885.80471.36320.28910.0970.05540.08680.093-0.1493-0.12020.08210.0207-0.06620.19240.0025-0.00580.17380.0160.122976.334160.4742112.8589
362.40171.085-0.07422.5436-0.44410.7661-0.07420.11990.1214-0.2290.07280.0743-0.03510.09960.01130.1920.0058-0.00670.13310.01130.086969.564766.6747110.8325
374.22480.12992.95221.856-1.78656.5805-0.21250.20960.41420.22440.0184-0.2094-0.49080.63530.23730.2146-0.0037-0.04610.2589-0.01590.334393.465370.3943127.6405
381.15410.55910.17241.79350.641.89590.0478-0.34610.07210.4155-0.0294-0.21270.01960.12180.02330.32920.0289-0.07610.3249-0.01620.209985.610461.5925139.6103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 36 )A5 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 70 )A37 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 166 )A71 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 199 )A167 - 199
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 234 )A200 - 234
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 360 )A235 - 360
7X-RAY DIFFRACTION7chain 'A' and (resid 361 through 385 )A361 - 385
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 36 )B3 - 36
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 70 )B37 - 70
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 125 )B71 - 125
11X-RAY DIFFRACTION11chain 'B' and (resid 126 through 166 )B126 - 166
12X-RAY DIFFRACTION12chain 'B' and (resid 167 through 199 )B167 - 199
13X-RAY DIFFRACTION13chain 'B' and (resid 200 through 234 )B200 - 234
14X-RAY DIFFRACTION14chain 'B' and (resid 235 through 270 )B235 - 270
15X-RAY DIFFRACTION15chain 'B' and (resid 271 through 291 )B271 - 291
16X-RAY DIFFRACTION16chain 'B' and (resid 292 through 331 )B292 - 331
17X-RAY DIFFRACTION17chain 'B' and (resid 332 through 360 )B332 - 360
18X-RAY DIFFRACTION18chain 'B' and (resid 361 through 383 )B361 - 383
19X-RAY DIFFRACTION19chain 'C' and (resid 5 through 36 )C5 - 36
20X-RAY DIFFRACTION20chain 'C' and (resid 37 through 70 )C37 - 70
21X-RAY DIFFRACTION21chain 'C' and (resid 71 through 100 )C71 - 100
22X-RAY DIFFRACTION22chain 'C' and (resid 101 through 166 )C101 - 166
23X-RAY DIFFRACTION23chain 'C' and (resid 167 through 234 )C167 - 234
24X-RAY DIFFRACTION24chain 'C' and (resid 235 through 270 )C235 - 270
25X-RAY DIFFRACTION25chain 'C' and (resid 271 through 291 )C271 - 291
26X-RAY DIFFRACTION26chain 'C' and (resid 292 through 331 )C292 - 331
27X-RAY DIFFRACTION27chain 'C' and (resid 332 through 360 )C332 - 360
28X-RAY DIFFRACTION28chain 'C' and (resid 361 through 380 )C361 - 380
29X-RAY DIFFRACTION29chain 'D' and (resid 6 through 36 )D6 - 36
30X-RAY DIFFRACTION30chain 'D' and (resid 37 through 69 )D37 - 69
31X-RAY DIFFRACTION31chain 'D' and (resid 70 through 100 )D70 - 100
32X-RAY DIFFRACTION32chain 'D' and (resid 101 through 125 )D101 - 125
33X-RAY DIFFRACTION33chain 'D' and (resid 126 through 166 )D126 - 166
34X-RAY DIFFRACTION34chain 'D' and (resid 167 through 199 )D167 - 199
35X-RAY DIFFRACTION35chain 'D' and (resid 200 through 234 )D200 - 234
36X-RAY DIFFRACTION36chain 'D' and (resid 235 through 270 )D235 - 270
37X-RAY DIFFRACTION37chain 'D' and (resid 271 through 291 )D271 - 291
38X-RAY DIFFRACTION38chain 'D' and (resid 292 through 380 )D292 - 380

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