[English] 日本語
Yorodumi
- PDB-3gfs: Structure of YhdA, K109D/D137K variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gfs
TitleStructure of YhdA, K109D/D137K variant
ComponentsFMN-dependent NADPH-azoreductase
KeywordsOXIDOREDUCTASE / FLAVOPROTEINS / QUINONE REDUCTASE / FLAVODOXIN / OLIGOMERIZATION / Flavoprotein / FMN / NADP
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / FMN binding / oxidoreductase activity / identical protein binding / cytosol
Similarity search - Function
NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-dependent NADPH-azoreductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsStaunig, N. / Gruber, K.
CitationJournal: Febs J. / Year: 2009
Title: A single intersubunit salt bridge affects oligomerization and catalytic activity in a bacterial quinone reductase
Authors: Binter, A. / Staunig, N. / Jelesarov, I. / Lohner, K. / Palfey, B.A. / Deller, S. / Gruber, K. / Macheroux, P.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FMN-dependent NADPH-azoreductase
B: FMN-dependent NADPH-azoreductase
C: FMN-dependent NADPH-azoreductase
D: FMN-dependent NADPH-azoreductase
E: FMN-dependent NADPH-azoreductase
F: FMN-dependent NADPH-azoreductase
G: FMN-dependent NADPH-azoreductase
H: FMN-dependent NADPH-azoreductase
I: FMN-dependent NADPH-azoreductase
J: FMN-dependent NADPH-azoreductase
K: FMN-dependent NADPH-azoreductase
L: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,58724
Polymers227,11012
Non-polymers5,47612
Water17,601977
1
A: FMN-dependent NADPH-azoreductase
C: FMN-dependent NADPH-azoreductase
I: FMN-dependent NADPH-azoreductase
J: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5298
Polymers75,7034
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FMN-dependent NADPH-azoreductase
D: FMN-dependent NADPH-azoreductase
G: FMN-dependent NADPH-azoreductase
H: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5298
Polymers75,7034
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: FMN-dependent NADPH-azoreductase
F: FMN-dependent NADPH-azoreductase
hetero molecules

K: FMN-dependent NADPH-azoreductase
L: FMN-dependent NADPH-azoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5298
Polymers75,7034
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Unit cell
Length a, b, c (Å)68.625, 170.132, 93.289
Angle α, β, γ (deg.)90.000, 92.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 106 / Label seq-ID: 3 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

NCS ensembles :
ID
1
A
3:106
108:169
2
and
or
)'
'chain
(resseq
resseq
D
5
G
8
J
11

-
Components

#1: Protein
FMN-dependent NADPH-azoreductase / Azobenzene reductase


Mass: 18925.869 Da / Num. of mol.: 12 / Mutation: K109D, D137K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: azr, BSU09340, yhdA / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O07529, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298 K / Method: batch crystallization / pH: 8.5
Details: 0.1 M Tris pH 8.5, 2.0 M Ammonium Sulfate, batch crystallization, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8148 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.105→30 Å / Num. all: 119393 / Num. obs: 119393 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 31.26 Å2 / Rsym value: 0.096
Reflection shellResolution: 2.105→2.16 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.46 / % possible all: 52.5

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1nni

1nni


Resolution: 2.105→29.341 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / SU ML: 0.3 / Isotropic thermal model: isotropic plus TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 23.63 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 6012 5.04 %RANDOM
Rwork0.185 ---
all0.187 119393 --
obs0.187 119393 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.257 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 148.24 Å2 / Biso mean: 36.237 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1-7.422 Å2-0 Å20.498 Å2
2---4.633 Å2-0 Å2
3----2.789 Å2
Refinement stepCycle: LAST / Resolution: 2.105→29.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15379 0 372 977 16728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216004
X-RAY DIFFRACTIONf_angle_d0.5821695
X-RAY DIFFRACTIONf_chiral_restr0.0392532
X-RAY DIFFRACTIONf_plane_restr0.0022726
X-RAY DIFFRACTIONf_dihedral_angle_d16.065865
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1277X-RAY DIFFRACTIONPOSITIONAL
12B1277X-RAY DIFFRACTIONPOSITIONAL0.433
13C1277X-RAY DIFFRACTIONPOSITIONAL0.6
14D1277X-RAY DIFFRACTIONPOSITIONAL0.58
15E1277X-RAY DIFFRACTIONPOSITIONAL0.626
16F1272X-RAY DIFFRACTIONPOSITIONAL0.608
17G1277X-RAY DIFFRACTIONPOSITIONAL0.635
18H1272X-RAY DIFFRACTIONPOSITIONAL0.503
19I1277X-RAY DIFFRACTIONPOSITIONAL0.684
110J1277X-RAY DIFFRACTIONPOSITIONAL0.579
111K1277X-RAY DIFFRACTIONPOSITIONAL0.663
112L1266X-RAY DIFFRACTIONPOSITIONAL0.533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.105-2.1290.354930.26614381531
2.129-2.1540.3181850.25233093494
2.154-2.1810.2921870.23336413828
2.181-2.2080.2981750.23436743849
2.208-2.2370.282200.22537904010
2.237-2.2680.2991900.21539034093
2.268-2.30.2532100.19838694079
2.3-2.3350.2392010.18938744075
2.335-2.3710.2471890.19539304119
2.371-2.410.2451990.19438934092
2.41-2.4510.2592060.19439454151
2.451-2.4960.2592090.18738174026
2.496-2.5440.2362460.20438804126
2.544-2.5960.2632120.20138874099
2.596-2.6520.2672060.19739174123
2.652-2.7140.2562100.1938484058
2.714-2.7820.2412020.1939094111
2.782-2.8570.2282110.19139194130
2.857-2.9410.2551840.20338914075
2.941-3.0360.2522190.19538944113
3.036-3.1440.2422250.1938914116
3.144-3.270.2291930.19639284121
3.27-3.4180.2222000.18639014101
3.418-3.5980.2031960.17339314127
3.598-3.8230.1942120.16238994111
3.823-4.1180.1742150.14738714086
4.118-4.5310.152140.1339184132
4.531-5.1830.1572140.13539244138
5.183-6.5180.1891930.17939354128
6.518-29.3430.1711960.16939554151
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2121-0.93590.30960.9168-0.69692.55490.01630.04990.2517-0.03960.00270.1226-0.373-0.2137-0.02910.19360.0186-0.01220.18670.00180.2389-37.2005-20.9774-21.9307
23.01760.5542.39011.30421.28972.14490.0596-0.62050.1650.1792-0.27290.20360.3393-0.42080.22460.20490.03230.0370.3071-0.0070.2495-41.0827-25.1758-6.7337
30.29630.020.00760.32960.02210.8657-0.036-0.0041-0.0086-0.01030.02-0.01120.0580.13990.01310.14090.0009-0.01730.1550.00390.2024-33.7143-33.6292-21.093
41.3508-0.56920.60650.3236-0.30632.20110.2222-0.0340.04640.0086-0.24210.079-0.3817-0.14910.04510.2555-0.0028-0.01990.23270.00110.1897-39.6983-27.383-35.0388
50.56710.4476-0.35760.6960.48530.7318-0.01550.12880.0177-0.16670.0588-0.0249-0.1660.0214-0.03260.1941-0.008-0.00850.19640.00680.181216.4553-8.07334.9734
6-0.96350.4028-0.06260.6276-0.24960.3812-0.00330.00330.060.0771-0.00360.057-0.0026-0.03250.01920.1294-0.0107-0.00430.2007-0.01950.182314.6024-11.582713.5256
70.78610.2512-0.34720.72940.5384-0.4550.0294-0.00870.04270.09240.0888-0.1187-0.13160.0795-0.07550.2816-0.03510.01910.205-0.0160.181516.2684-0.345418.8792
81.4732-2.51871.1751.98270.1092.4443-0.15240.0430.64330.71910.2131-0.6448-0.4820.48590.0180.2819-0.076-0.03740.268-0.01650.279728.3018-6.721524.324
9-0.0269-0.47370.24720.0927-0.27111.14040.0878-0.10230.12350.2203-0.21620.061-0.18010.2060.12280.1234-0.0212-0.0160.21360.04160.1907-15.8234-32.1502-2.3712
100.1514-0.21150.4105-0.82760.54021.2004-0.1085-0.01690.10890.18350.01580.0459-0.34460.12810.10990.1655-0.0533-0.07130.18840.02060.2401-14.5853-26.1841-5.8822
11-0.31180.03380.46261.3798-0.49181.0733-0.00860.134-0.046-0.0828-0.0755-0.07970.04190.27240.06830.1314-0.00580.00380.27360.01550.1983-15.3318-31.3848-14.5773
120.7719-0.23631.38660.4526-0.5332.31740.10220.1792-0.0771-0.0549-0.0411-0.01360.31520.3311-0.08980.20760.0337-0.03340.2184-0.00330.2238-10.7332-43.9721-2.7234
139.5925-3.32892.58033.3737-0.50222.7790.61880.2928-0.284-0.4543-0.27320.35950.1753-0.0942-0.2810.13570.0006-0.08040.17730.00980.3242-12.7677-20.96699.1869
141.11930.22630.2065-0.07580.72070.0615-0.00690.2372-0.1644-0.05370.01620.04030.11670.0323-0.03550.1991-0.0123-0.03460.23530.00140.1992-6.2192-27.16.3456
150.08370.5876-0.13061.3334-1.10061.2451-0.03190.07460.0210.05810.06070.1407-0.11120.044-0.03730.1319-0.0022-0.00560.1919-0.00250.1592-4.0569-14.17438.9967
16-0.110.74171.13471.5712-0.03930.71180.0296-0.13020.05390.08380.02550.2864-0.0228-0.0399-0.03650.16110.00350.05680.2319-0.00210.2429-9.7682-25.026418.7909
170.861-0.01911.01370.3814-0.1391.6580.03530.0776-0.0527-0.2950.02510.0065-0.09370.0539-0.01840.2636-0.0103-0.03280.23120.0230.212712.7797-52.22744.0086
183.20741.82990.51852.66380.41980.1584-0.1412-1.0233-0.00760.4191-0.31520.0645-0.257-0.33720.29670.28790.0431-0.09540.3072-0.02490.22788.1967-39.227213.2041
190.5224-0.2625-0.23391.32380.02090.2812-0.05920.0701-0.0072-0.10490.02380.00340.0817-0.03490.02060.166-0.0221-0.00180.16570.00780.158714.5488-59.852610.8794
201.54351.02050.42031.6034-0.35561.0549-0.3384-0.0777-0.074-0.26150.25340.25680.1464-0.240.01710.2706-0.0688-0.01370.25780.02560.32493.4686-68.97759.0924
214.6637-3.4171-0.25570.5656-1.0441.78950.084-0.59140.15510.06490.1704-0.62610.15530.1833-0.37520.1635-0.0592-0.03990.2453-0.04460.324139.3191-45.106422.8395
220.48060.85690.22110.46090.50970.61370.01260.01490.0726-0.22670.0379-0.057-0.24540.0055-0.02220.2651-0.0061-0.01660.1950.00590.249131.3025-40.387622.453
230.3848-0.09410.00250.8051-0.4991.3292-0.02630.0816-0.0245-0.03830.0185-0.15140.03380.07120.02070.1581-0.00460.01730.15890.00110.204932.6125-51.122718.0625
240.017-0.37940.40412.5040.67540.8254-0.1119-0.00870.09720.46350.1214-0.38120.19370.0617-0.0260.19780.0065-0.04220.24660.02290.220135.6576-47.185235.8662
252.84970.49620.25311.8296-0.16790.07260.00240.36730.18020.53590.08690.00540.0005-0.1033-0.05280.28190.0042-0.00960.2076-0.01550.183411.6311-21.264845.5553
260.9394-0.26670.33371.2578-0.46830.6754-0.0741-0.14060.07130.50020.0179-0.0417-0.2862-0.08150.05820.34570.0213-0.02340.199-0.02870.143112.0601-15.764445.1766
270.8604-0.28650.69411.34730.74211.05360.00630.0677-0.06630.07540.02220.0710.05970.043-0.02240.15440.01030.00110.1845-0.01660.152812.5272-24.844934.8813
282.6572-4.15522.50684.68062.46076.05850.1110.37730.2498-0.29110.1346-0.57340.65641.0932-0.14830.24720.0097-0.01530.32230.03020.313626.5749-20.81832.7196
290.36170.0298-0.4241.1872-0.03980.9532-0.088-0.06770.11450.57780.28040.3054-0.39990.0724-0.17250.43690.10120.14890.18340.00480.2303-8.7441-0.449144.1252
300.07310.3692-0.1520.98880.13140.56980.0381-0.0961-0.03510.2706-0.00160.1013-0.0572-0.0354-0.0460.30910.05820.10440.22660.01760.2195-8.3339-10.742641.4425
311.4297-0.1106-0.69150.20270.48330.9622-0.10890.2303-0.22580.00720.0910.0752-0.03030.05360.01730.21260.02610.05650.1877-0.00070.1892-5.3055-7.355229.8171
320.5279-0.5111-0.36940.22640.44562.03680.00470.0805-0.023-0.24410.10610.1157-0.6601-0.1595-0.13050.38180.11970.08210.28180.06330.2318-11.70266.852831.2455
330.2341-0.1245-0.1175-0.896-0.22850.6210.0583-0.0154-0.22080.0467-0.04250.01170.4936-0.0456-0.00850.3976-0.0165-0.02050.16450.01940.2414-35.5172-65.9561-22.0568
340.7460.0048-0.29220.907-0.75831.4509-0.07930.1325-0.1239-0.2120.0454-0.01550.44860.00120.02810.336-0.01670.00910.2113-0.030.1977-32.5044-58.4066-32.334
351.24380.44840.16070.44951.83382.23360.0008-0.10840.07840.205-0.00250.03750.26830.0904-0.00940.23470.02020.02990.1684-0.00830.1855-34.4355-55.6708-16.7213
36-0.8469-2.00331.08871.2760.41053.8260.2297-0.11070.2339-0.058-0.12770.4073-0.3425-0.9284-0.17820.2491-0.02890.0490.41290.03060.3194-48.0457-51.1253-20.2741
370.48360.2311-0.47411.5255-0.70111.3171-0.06870.1922-0.0203-0.6687-0.0524-0.08480.60290.59320.13290.41610.0840.07230.47110.00120.209-11.7359-55.2256-40.149
380.07220.3051-0.57530.93350.78032.1105-0.0285-0.0834-0.0640.0449-0.065-0.12320.35610.57440.08780.24370.11280.05590.37570.03080.1841-12.2068-55.0897-31.3892
391.0567-0.7146-0.32062.1006-0.25711.7645-0.1618-0.14750.03990.20220.10170.1218-0.32910.6548-0.07310.21220.00510.02260.3613-0.03760.2262-17.8052-45.97-27.0381
402.0753-0.312-1.99382.4266-1.30721.12370.02120.14410.3008-0.4968-0.0617-0.38530.17910.26250.06630.3706-0.04330.08030.41020.08280.3503-9.0413-39.6282-38.4844
410.9055-0.77680.30941.8808-1.12740.94790.24650.2077-0.1515-0.9637-0.1903-0.00220.63070.04150.01330.5850.0710.07370.2090.00750.2082-15.53039.3264-42.3559
420.78860.3134-0.34251.3498-0.11950.15420.08070.0291-0.0589-0.5463-0.1117-0.03540.1808-0.00920.04980.37290.02830.05830.1446-0.00080.1471-14.14072.8907-33.4155
430.5222-0.518-0.01910.69350.51020.56120.1352-0.01330.154-0.2863-0.1083-0.2037-0.12110.0162-0.06490.3020.01980.09140.16310.01090.2027-12.661917.4409-34.3391
441.9572-3.46620.14932.2155-2.43435.7744-0.1810.08730.6015-0.2039-0.1985-0.81220.36110.59020.33060.29950.04270.08370.32970.02260.35330.752718.0936-28.9863
452.81720.64062.14510.1297-1.33873.32720.2354-0.20780.1486-0.4035-0.2372-0.08690.828-0.10140.00250.2845-0.0521-0.03380.13620.02820.2918-34.249-0.5453-21.5194
460.71420.5636-0.33220.9814-0.76581.389-0.12880.1125-0.2348-0.51530.14750.61080.5031-0.1254-0.05420.4637-0.0577-0.08740.2010.00550.4381-37.6351-0.0963-30.8291
470.2208-0.0146-0.2041.9488-0.44450.5420.01320.0269-0.0505-0.32540.13340.32460.1463-0.0277-0.13280.2516-0.0218-0.06270.17030.00930.2429-34.734910.661-25.5993
48-0.29731.4397-0.41621.829-0.94361.4722-0.0147-0.2752-0.31790.06320.0810.55060.1114-0.3731-0.07510.2973-0.04810.11180.36860.05860.4682-42.30966.8723-11.5754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1-43
2X-RAY DIFFRACTION2chain A and resid 44-65
3X-RAY DIFFRACTION3chain A and resid 66-135
4X-RAY DIFFRACTION4chain A and resid 136-171
5X-RAY DIFFRACTION5chain B and resid 1-53
6X-RAY DIFFRACTION6chain B and resid 54-117
7X-RAY DIFFRACTION7chain B and resid 118-160
8X-RAY DIFFRACTION8chain B and resid 161-171
9X-RAY DIFFRACTION9chain C and resid 1-18
10X-RAY DIFFRACTION10chain C and resid 19-47
11X-RAY DIFFRACTION11chain C and resid 48-133
12X-RAY DIFFRACTION12chain C and resid 134-168
13X-RAY DIFFRACTION13chain D and resid 1-6
14X-RAY DIFFRACTION14chain D and resid 7-38
15X-RAY DIFFRACTION15chain D and resid 39-117
16X-RAY DIFFRACTION16chain D and resid 118-168
17X-RAY DIFFRACTION17chain E and resid 1-46
18X-RAY DIFFRACTION18chain E and resid 47-59
19X-RAY DIFFRACTION19chain E and resid 60-153
20X-RAY DIFFRACTION20chain E and resid 154-171
21X-RAY DIFFRACTION21chain F and resid 1-6
22X-RAY DIFFRACTION22chain F and resid 7-44
23X-RAY DIFFRACTION23chain F and resid 45-136
24X-RAY DIFFRACTION24chain F and resid 137-168
25X-RAY DIFFRACTION25chain G and resid 1-11
26X-RAY DIFFRACTION26chain G and resid 12-111
27X-RAY DIFFRACTION27chain G and resid 112-159
28X-RAY DIFFRACTION28chain G and resid 160-171
29X-RAY DIFFRACTION29chain H and resid 1-43
30X-RAY DIFFRACTION30chain H and resid 44-110
31X-RAY DIFFRACTION31chain H and resid 111-138
32X-RAY DIFFRACTION32chain H and resid 139-168
33X-RAY DIFFRACTION33chain I and resid 1-35
34X-RAY DIFFRACTION34chain I and resid 36-111
35X-RAY DIFFRACTION35chain I and resid 112-159
36X-RAY DIFFRACTION36chain I and resid 160-171
37X-RAY DIFFRACTION37chain J and resid 1-47
38X-RAY DIFFRACTION38chain J and resid 48-109
39X-RAY DIFFRACTION39chain J and resid 110-125
40X-RAY DIFFRACTION40chain J and resid 126-168
41X-RAY DIFFRACTION41chain K and resid 1-20
42X-RAY DIFFRACTION42chain K and resid 21-91
43X-RAY DIFFRACTION43chain K and resid 92-160
44X-RAY DIFFRACTION44chain K and resid 161-171
45X-RAY DIFFRACTION45chain L and resid 1-16
46X-RAY DIFFRACTION46chain L and resid 17-54
47X-RAY DIFFRACTION47chain L and resid 55-139
48X-RAY DIFFRACTION48chain L and resid 140-168

+
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