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- PDB-7jh4: Crystal structure of NAD(P)H-flavin oxidoreductase (NfoR) from S.... -

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Basic information

Entry
Database: PDB / ID: 7jh4
TitleCrystal structure of NAD(P)H-flavin oxidoreductase (NfoR) from S. aureus complexed with reduced FMN and NAD+
ComponentsNAD(P)H-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / FMN / FMN reductase / chromate reductase
Function / homology
Function and homology information


: / 2,4,6-trinitrotoluene catabolic process / Oxidoreductases / oxidoreductase activity / cytosol
Similarity search - Function
Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like
Similarity search - Domain/homology
Chem-FNR / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P)H-dependent oxidoreductase / Putative NAD(P)H nitroreductase SAOUHSC_02829
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZheng, Y. / O'Neill, A.G. / Beaupre, B.A. / Liu, D. / Moran, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1904480 United States
CitationJournal: Appl.Environ.Microbiol. / Year: 2020
Title: NfoR: Chromate Reductase or Flavin Mononucleotide Reductase?
Authors: O'Neill, A.G. / Beaupre, B.A. / Zheng, Y. / Liu, D. / Moran, G.R.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P)H-dependent oxidoreductase
B: NAD(P)H-dependent oxidoreductase
C: NAD(P)H-dependent oxidoreductase
D: NAD(P)H-dependent oxidoreductase
E: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,64212
Polymers127,0235
Non-polymers3,6197
Water13,872770
1
A: NAD(P)H-dependent oxidoreductase
B: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3905
Polymers50,8092
Non-polymers1,5803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-55 kcal/mol
Surface area17450 Å2
MethodPISA
2
C: NAD(P)H-dependent oxidoreductase
hetero molecules

C: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0536
Polymers50,8092
Non-polymers2,2444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10210 Å2
ΔGint-61 kcal/mol
Surface area16930 Å2
MethodPISA
3
D: NAD(P)H-dependent oxidoreductase
E: NAD(P)H-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7264
Polymers50,8092
Non-polymers9172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-52 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.802, 84.844, 107.701
Angle α, β, γ (deg.)90.000, 124.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-441-

HOH

21C-451-

HOH

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Components

#1: Protein
NAD(P)H-dependent oxidoreductase / NfoR / NAD(P)H-flavin oxidoreductase


Mass: 25404.699 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: LZ-01 / Gene: nfoR, E5491_14200 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A220YLK3, UniProt: Q2FVA4*PLUS, Oxidoreductases
#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H23N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG4000, 210 mM ammonium acetate, 100 mM sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 21, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 84335 / % possible obs: 95.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Χ2: 0.949 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.053.10.80232840.5880.5160.9570.93475.1
2.05-2.093.30.71335900.6830.4460.8430.96581.5
2.09-2.133.40.65938070.7310.4010.7730.94887.5
2.13-2.183.50.55940340.8140.3390.6550.98592.2
2.18-2.223.60.49341820.8520.2990.5770.98595.5
2.22-2.273.60.45342910.8650.2740.531.00298.1
2.27-2.333.70.37143270.9240.2220.4330.99399
2.33-2.393.80.31743650.9470.1890.3690.97699.1
2.39-2.473.80.25843580.9630.1530.30.99699.2
2.47-2.543.80.2142970.9750.1250.2450.97399.3
2.54-2.643.80.17943840.9810.1060.2081.00299.5
2.64-2.743.80.14343870.9850.0850.1671.00999.5
2.74-2.873.80.11143690.9910.0660.1290.97199.3
2.87-3.023.80.08743790.9930.0520.1020.94199.7
3.02-3.213.80.06243690.9960.0370.0730.90199.5
3.21-3.453.80.04743930.9970.0280.0540.85699.7
3.45-3.83.80.03944090.9970.0230.0450.80199.7
3.8-4.353.80.03444020.9980.020.0390.73899.7
4.35-5.483.80.03644370.9970.0220.0420.82999.6
5.48-503.60.04542710.9940.0280.0531.22794.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
REFMAC5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HAY
Resolution: 2→36.1 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 3418 4.89 %
Rwork0.1694 66469 -
obs0.1712 69887 79.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.57 Å2 / Biso mean: 34.5193 Å2 / Biso min: 8.68 Å2
Refinement stepCycle: final / Resolution: 2→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8868 0 278 770 9916
Biso mean--26.54 38.22 -
Num. residues----1114
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.030.313570.226996828
2.03-2.060.2616610.227127037
2.06-2.090.2961900.2271153945
2.09-2.130.2881940.2172171550
2.13-2.160.2398920.2037187854
2.16-2.20.27451160.2028204260
2.2-2.250.25941000.2026222164
2.25-2.290.2242970.1916239868
2.29-2.340.24211420.1882253874
2.34-2.40.22791460.1876269778
2.4-2.460.19351380.1925287783
2.46-2.520.25091500.1915304388
2.52-2.60.22921710.1995328895
2.6-2.680.2451790.1926344499
2.68-2.780.2341760.1836344899
2.78-2.890.22221630.18593440100
2.89-3.020.24051900.18783478100
3.02-3.180.20942130.17153404100
3.18-3.380.20961750.15893475100
3.38-3.640.16192000.15053453100
3.64-40.18541640.15113484100
4-4.580.18281830.13243475100
4.58-5.770.1911470.153541100
5.77-36.10.17311740.1638335394
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)
16.37073.1271-2.32562.6241.39256.74690.065-0.8514-0.75580.6192-0.2555-0.66990.79960.48560.16040.28390.0656-0.09310.420.11670.432339.6645-14.796354.61
21.42820.0254-0.2880.855-0.05251.3591-0.11510.0994-0.0026-0.24480.0747-0.3044-0.04030.17570.02950.20.00720.11110.17160.05930.287934.51-8.781731.6513
31.83311.002-0.30512.57770.23392.1392-0.19260.0506-0.1205-0.14280.12410.28730.2733-0.26480.07320.1816-0.04620.04360.22430.04330.319510.5997-22.310631.6996
41.89680.0971-0.04951.29340.20921.8154-0.16850.24050.1052-0.30280.096-0.0842-0.13530.01430.04310.1518-0.0080.06240.11360.07120.235127.663-6.602531.8528
53.5025-0.2807-0.73022.08430.58613.23850.0613-0.73870.29010.3631-0.0386-0.2807-0.23470.28410.01720.24860.0264-0.07490.2910.01080.27832.1856-3.770555.4322
61.11820.92540.01783.5596-0.24663.14450.09550.0624-0.3344-0.2017-0.1395-1.0902-0.02820.68580.04160.35970.10740.12030.28650.11080.588339.031-24.223744.4196
71.4936-0.04860.48542.3991-0.48833.79060.119-0.463-0.44390.4481-0.02820.26150.7368-0.4106-0.09370.3411-0.02260.09830.29240.11460.349721.3978-27.468554.8331
81.27830.5065-0.03641.2357-0.0961.35550.0041-0.32620.07140.3455-0.00540.27930.0553-0.20750.02260.1940.04470.12760.25670.03120.295818.4064-11.290954.1096
90.61131.6554-0.49214.4853-1.32820.4059-0.07670.0659-0.2728-0.0366-0.0534-0.46690.07050.40170.12760.22140.0660.04610.3104-0.07320.367627.532910.372452.5188
100.91861.7040.77855.9843.63854.261-0.05180.00970.3978-0.26930.3246-0.011-0.23840.1762-0.25310.21350.05910.11220.20520.05140.505524.276911.392538.9414
110.6920.05510.24320.52410.04270.52840.0322-0.26070.10390.20650.00890.2376-0.0017-0.24180.03670.13280.04510.13670.25790.04170.325616.4945-10.004548.8703
120.14690.2837-0.43881.882-3.42138.1596-0.17-0.0897-0.4899-0.25270.15710.07611.1009-0.41790.02630.35670.00080.14520.23820.07020.499224.3213-30.643143.6513
138.9996.4093-5.55144.6525-4.436.0202-0.07340.2255-0.4145-0.2640.0669-0.30490.1660.2187-0.01390.36170.00550.18080.1929-0.05760.428236.9144-16.95824.7931
147.26431.79942.00893.03053.456.8765-0.45440.51290.6819-0.47250.09080.1663-0.93040.23490.36570.6152-0.1055-0.29090.3153-0.05010.437164.597846.352444.6011
151.217-0.24280.75660.45910.26721.1949-0.2867-0.38390.27790.26750.09420.0288-0.4356-0.22030.21640.60530.1731-0.29170.3569-0.1560.298258.912638.72563.0813
161.1278-0.09390.46450.3908-0.04411.6935-0.2735-0.28760.11320.33290.03930.0999-0.202-0.3720.02930.40980.1344-0.1810.2816-0.04620.147948.752128.01255.385
175.2976-1.31342.87742.9463-0.11635.5184-0.21430.62580.5829-0.5329-0.02410.4367-0.4512-0.37320.19780.22950.0287-0.13910.4630.00170.380834.700223.591137.4987
183.2413-0.65070.29533.2101-0.31233.20730.05270.397-0.2933-0.3844-0.0340.37-0.0006-0.3113-0.03790.3268-0.0871-0.10660.3377-0.05910.191744.711315.264431.747
190.6324-0.08340.17720.29170.05370.5392-0.2695-0.25590.01080.15030.01670.0331-0.2336-0.1611-0.29620.2560.1134-0.26220.22310.03270.062352.17423.85753.4599
201.1604-1.4918-2.39771.91493.07694.9903-0.0445-0.55560.28450.21650.3593-0.24330.27180.7307-0.4080.66410.0201-0.29170.3939-0.14940.447969.575337.731356.9687
215.27921.8124-0.36193.0232.55043.0026-0.18710.62130.7203-0.46690.1556-0.1061-0.64710.26760.03230.5388-0.276-0.08620.44920.14310.597573.788432.975231.2725
225.6791-1.12524.7068.7079-0.98275.93990.19230.44660.4328-0.4431-0.0047-1.1806-0.06041.0036-0.160.457-0.25020.17010.56490.02770.556168.370214.1617-4.9258
230.9086-0.09150.1142.1357-1.29862.3224-0.00730.1430.0158-0.5852-0.1485-0.2381-0.09020.22650.14340.4518-0.02150.09910.21290.00140.217853.8545.8002-11.8791
241.8989-0.64850.25192.1794-0.76362.2467-0.0881-0.0426-0.0861-0.43210.12320.23120.0415-0.3288-0.00020.4325-0.0235-0.06970.2184-0.02320.133342.39061.8383-9.1602
254.2521.01320.02362.5564-0.05924.96520.03230.4085-0.6503-0.32740.0271-0.59150.59420.6419-0.04350.69290.03560.1490.3199-0.12010.432956.2154-20.9354-10.8432
261.7795-0.0969-0.32562.02210.18681.6617-0.03390.0948-0.3134-0.2963-0.020.00780.42670.06180.03510.3506-0.0361-0.00220.1764-0.0320.142848.7563-6.0688-2.5842
271.7635-1.88653.74352.1752-3.66098.7197-0.2826-0.130.38020.137-0.0786-0.3484-1.0866-0.00740.35530.379-0.1098-0.01540.30080.0050.261554.57620.0106-0.4255
289.3804-4.36352.72968.5413-2.88755.8494-0.1106-0.50070.38830.07950.2109-1.06460.18560.8814-0.09390.4781-0.1201-0.16310.7561-0.08020.570370.6047.279914.6762
294.8623-1.8727-1.52072.01492.3686.95310.18860.64570.5673-0.476-0.1715-0.4425-0.38610.4206-0.05570.4607-0.08490.33320.7639-0.00310.664167.53844.8503-14.8991
303.05741.62961.10971.23750.53210.4115-0.0146-0.0496-0.28660.0510.1254-0.75270.1860.594-0.10020.38520.19980.19970.9569-0.00891.011676.7208-5.33260.5395
312.3279-0.69910.19642.632-0.11381.1275-0.1231-0.1884-0.15980.09250.0648-0.92690.18820.88040.05630.23830.0147-0.03220.62730.00730.477766.46062.177810.003
320.8161.14480.42152.436-0.27552.17650.0772-0.0669-0.12120.1191-0.0663-0.45560.00430.53480.00290.2257-0.0438-0.05790.32780.01670.210857.80463.542213.1053
331.77870.1027-0.19922.37882.25562.2605-0.03780.08460.02510.0613-0.13890.4233-0.2989-0.28710.17350.2575-0.0378-0.0230.23360.01650.166139.06298.581711.1801
341.5368-0.05180.69012.21850.40380.82120.0038-0.3432-0.23970.19950.0155-0.65240.42490.71070.0150.24850.0584-0.04060.4250.04160.321560.5934-3.39329.6652
357.28332.47863.47940.84371.18231.67690.27060.7227-0.6950.0110.1992-0.56160.47530.9349-0.4350.49160.13910.18680.8373-0.03240.744670.8918-9.736-9.4479
368.8272-4.52232.0926.10523.29055.51860.08250.83230.1107-0.7267-0.2986-0.048-0.14890.18180.18510.7212-0.09610.03340.4081-0.05540.161147.9121-1.4904-20.178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )A1 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 95 )A15 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 132 )A96 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 197 )A133 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 223 )A198 - 223
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 14 )B1 - 14
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 28 )B15 - 28
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 95 )B29 - 95
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 109 )B96 - 109
10X-RAY DIFFRACTION10chain 'B' and (resid 110 through 132 )B110 - 132
11X-RAY DIFFRACTION11chain 'B' and (resid 133 through 197 )B133 - 197
12X-RAY DIFFRACTION12chain 'B' and (resid 198 through 211 )B198 - 211
13X-RAY DIFFRACTION13chain 'B' and (resid 212 through 223 )B212 - 223
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 14 )C1 - 14
15X-RAY DIFFRACTION15chain 'C' and (resid 15 through 28 )C15 - 28
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 95 )C29 - 95
17X-RAY DIFFRACTION17chain 'C' and (resid 96 through 109 )C96 - 109
18X-RAY DIFFRACTION18chain 'C' and (resid 110 through 132 )C110 - 132
19X-RAY DIFFRACTION19chain 'C' and (resid 133 through 197 )C133 - 197
20X-RAY DIFFRACTION20chain 'C' and (resid 198 through 211 )C198 - 211
21X-RAY DIFFRACTION21chain 'C' and (resid 212 through 223 )C212 - 223
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 14 )D1 - 14
23X-RAY DIFFRACTION23chain 'D' and (resid 15 through 50 )D15 - 50
24X-RAY DIFFRACTION24chain 'D' and (resid 51 through 95 )D51 - 95
25X-RAY DIFFRACTION25chain 'D' and (resid 96 through 109 )D96 - 109
26X-RAY DIFFRACTION26chain 'D' and (resid 110 through 197 )D110 - 197
27X-RAY DIFFRACTION27chain 'D' and (resid 198 through 211 )D198 - 211
28X-RAY DIFFRACTION28chain 'D' and (resid 212 through 223 )D212 - 223
29X-RAY DIFFRACTION29chain 'E' and (resid 1 through 14 )E1 - 14
30X-RAY DIFFRACTION30chain 'E' and (resid 15 through 28 )E15 - 28
31X-RAY DIFFRACTION31chain 'E' and (resid 29 through 68 )E29 - 68
32X-RAY DIFFRACTION32chain 'E' and (resid 69 through 109 )E69 - 109
33X-RAY DIFFRACTION33chain 'E' and (resid 110 through 132 )E110 - 132
34X-RAY DIFFRACTION34chain 'E' and (resid 133 through 197 )E133 - 197
35X-RAY DIFFRACTION35chain 'E' and (resid 198 through 211 )E198 - 211
36X-RAY DIFFRACTION36chain 'E' and (resid 212 through 223 )E212 - 223

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