[English] 日本語
Yorodumi
- PDB-6rkf: Structure of human DASPO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rkf
TitleStructure of human DASPO
ComponentsD-aspartate oxidase
KeywordsFLAVOPROTEIN / D-aspartate oxidase / D-aspartate / oxidase / DASPO / hDASPO / DDO / hDDO Oxidoreductase / FAD
Function / homology
Function and homology information


D-aspartate oxidase / D-aspartate oxidase activity / : / insemination / protein targeting to peroxisome / D-amino-acid oxidase activity / D-amino acid catabolic process / aspartate metabolic process / grooming behavior / aspartate catabolic process ...D-aspartate oxidase / D-aspartate oxidase activity / : / insemination / protein targeting to peroxisome / D-amino-acid oxidase activity / D-amino acid catabolic process / aspartate metabolic process / grooming behavior / aspartate catabolic process / Glyoxylate metabolism and glycine degradation / hormone metabolic process / peroxisomal matrix / FAD binding / Peroxisomal protein import / peroxisome / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...D-amino acid oxidase, conserved site / D-amino-acid oxidase / D-amino acid oxidases signature. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / D-aspartate oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.219 Å
AuthorsChaves-Sanjuan, A. / Nardini, M.
CitationJournal: Faseb J. / Year: 2020
Title: Structure and kinetic properties of human d-aspartate oxidase, the enzyme-controlling d-aspartate levels in brain.
Authors: Molla, G. / Chaves-Sanjuan, A. / Savinelli, A. / Nardini, M. / Pollegioni, L.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-aspartate oxidase
B: D-aspartate oxidase
C: D-aspartate oxidase
D: D-aspartate oxidase
E: D-aspartate oxidase
F: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,10623
Polymers232,2846
Non-polymers5,82217
Water3,225179
1
A: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8095
Polymers38,7141
Non-polymers1,0954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5923
Polymers38,7141
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7144
Polymers38,7141
Non-polymers1,0003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5923
Polymers38,7141
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5923
Polymers38,7141
Non-polymers8782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: D-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8095
Polymers38,7141
Non-polymers1,0954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.397, 159.715, 288.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
D-aspartate oxidase / / DDO


Mass: 38714.043 Da / Num. of mol.: 6 / Mutation: C141Y, C143G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDO / Production host: Escherichia coli (E. coli) / References: UniProt: Q99489, D-aspartate oxidase

-
Non-polymers , 5 types, 196 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.96 Å3/Da / Density % sol: 58.51 % / Description: Rod-shaped yellow crystals
Crystal growTemperature: 291 K / Method: evaporation / pH: 8 / Details: 20 mM Tris-HCl pH 8.0, 10 % glycerol, 50 mM NaCl

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.219→144.29 Å / Num. obs: 23134 / % possible obs: 53.5 % / Observed criterion σ(I): 1.6 / Redundancy: 5.8 % / CC1/2: 0.986 / Rpim(I) all: 0.133 / Net I/σ(I): 5.9
Reflection shellResolution: 3.219→3.66 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 114 / CC1/2: 0.535 / Rpim(I) all: 0.518 / % possible all: 8.7

-
Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAO
Resolution: 3.219→93.002 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.97
RfactorNum. reflection% reflection
Rfree0.2708 1203 5.21 %
Rwork0.2307 --
obs0.2328 23111 53.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.219→93.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15568 0 388 179 16135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416401
X-RAY DIFFRACTIONf_angle_d0.72722388
X-RAY DIFFRACTIONf_dihedral_angle_d25.6195771
X-RAY DIFFRACTIONf_chiral_restr0.0522447
X-RAY DIFFRACTIONf_plane_restr0.0052816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2186-3.34750.50260.3712132X-RAY DIFFRACTION3
3.3475-3.49990.2485190.3366399X-RAY DIFFRACTION9
3.4999-3.68440.4043330.2862706X-RAY DIFFRACTION16
3.6844-3.91520.2811810.27481218X-RAY DIFFRACTION27
3.9152-4.21750.30931330.24342437X-RAY DIFFRACTION54
4.2175-4.64190.25181830.21593528X-RAY DIFFRACTION77
4.6419-5.31360.27392260.21574180X-RAY DIFFRACTION92
5.3136-6.69430.28062590.25314594X-RAY DIFFRACTION100
6.6943-93.04070.24542630.21434714X-RAY DIFFRACTION99
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)
10.46720.04570.02661.8355-0.30260.7768-0.12410.0741-0.07660.0048-0.01990.30460.1561-0.2449-0.23120.0087-0.07260.07070.3399-0.05180.1818-39.68-37.9899-24.3248
20.3118-0.4666-0.08311.1944-0.04690.0788-0.14850.0538-0.3648-0.2810.09060.29830.2265-0.0510.03760.3723-0.12540.21660.33980.06080.2094-29.164-35.196-19.6574
30.5976-0.01380.08190.9641-0.28750.43090.0401-0.1944-0.06290.01830.18760.3210.143-0.09630.64240.08490.1520.08180.2656-0.1557-0.0537-19.7034-42.3993-4.7652
40.0216-0.0546-0.01230.26850.20690.1939-0.0889-0.09830.141-0.0234-0.2267-0.0672-0.0863-0.02-0.26770.3924-0.1526-0.06310.3743-0.02260.2598-6.9812-39.7714-2.8621
50.1856-0.0557-0.20680.0861-0.03260.37750.36940.06530.1595-0.40540.03690.2897-0.2139-0.61480.0330.37560.0456-0.00880.44490.0310.3636-35.0988-35.0473-29.7353
60.021-0.0496-0.05730.312-0.03830.51790.14350.1816-0.1431-0.00750.11670.03020.0222-0.20420.6855-0.0487-0.1555-0.19810.137-0.13880.1221-26.3199-24.1342-19.9082
70.62040.2605-0.10.26810.13781.9826-0.2839-0.1115-0.1117-0.149-0.13030.02810.0603-0.1229-1.51510.2651-0.20980.10360.3262-0.14040.1197-9.5278-32.0991-15.3687
80.08040.0161-0.05480.01770.01930.14270.0207-0.00760.08760.0564-0.0635-0.16880.11950.0539-0.02530.67690.21060.1080.23550.00730.3626-0.0296-30.2139-15.7347
90.13520.0178-0.16550.26890.01470.21820.07110.3255-0.00490.12480.04630.14050.0743-0.17620.27090.11080.22330.21980.52840.05460.3738-37.2032-30.2324-17.1384
100.6101-0.19450.24850.23150.19430.38990.1307-0.1199-0.34820.1297-0.39-0.05360.1469-0.052-0.2381-0.0026-0.011-0.15260.43050.17610.05518.9801-60.0252-11.3915
110.8244-0.3497-0.22910.78760.37370.6472-0.1588-0.36410.15110.28770.3893-0.1760.19770.19030.33880.3831-0.0088-0.16580.31770.08220.1739-2.823-56.3821-1.7864
120.15790.04550.14680.13170.15010.22390.1248-0.0976-0.17960.1382-0.0160.04030.18610.04060.10120.13-0.1358-0.24240.20270.05760.23517.3957-53.2811-12.1178
130.5594-0.2189-0.40770.94250.14990.31120.0926-0.05380.04160.15260.0581-0.15580.01430.25260.38820.3004-0.0685-0.11780.47510.0290.178827.697-67.0594-16.6754
140.10750.1615-0.00420.26390.04170.36110.0855-0.0918-0.25910.2373-0.1563-0.32480.12810.3012-0.30360.2032-0.1246-0.57670.0849-0.2027-0.4003-0.6804-66.6128-16.1259
150.0017-0.01150.00570.0726-0.05930.0750.1298-0.1263-0.1431-0.00330.0510.07580.0479-0.14670.09360.1165-0.10140.02060.3633-0.09060.5199-13.2074-66.6981-19.8433
160.47050.10260.06940.27960.02120.00340.20560.1586-0.26630.3493-0.02910.06770.23780.23070.05530.39360.013-0.0730.48040.07830.181316.5602-69.2203-10.8799
170.5304-0.01810.03560.4063-0.47070.7045-0.0624-0.25370.2490.1499-0.19160.0196-0.13660.0528-1.47780.4751-0.1709-0.16960.351-0.04170.339227.4276-59.4972-1.1883
180.12440.00520.09930.10110.05190.08430.128-0.1782-0.20540.06850.0167-0.16480.2481-0.12480.32440.6559-0.2948-0.14460.2078-0.03340.2398-17.2068-71.7246-35.5246
190.2154-0.29930.05640.4804-0.16180.1112-0.05840.06590.1480.145-0.0269-0.2773-0.00970.1439-0.1810.1644-0.0303-0.20930.1655-0.13880.1266-15.5637-64.3797-55.2923
200.30940.0880.30720.02810.07830.420.2221-0.0742-0.18270.07920.05770.03740.2434-0.06680.62710.3274-0.3232-0.34290.38920.10410.1325-28.1336-67.8945-53.7002
210.3368-0.0694-0.08420.0945-0.03730.05290.29560.1172-0.1838-0.1158-0.1276-0.07210.2116-0.29410.00170.40620.0308-0.05870.2858-0.04080.4585-25.1941-57.3147-61.0825
220.07770.0309-0.1030.09150.05750.3893-0.10210.18470.0536-0.0443-0.00640.0859-0.11880.33280.20550.0949-0.0168-0.00490.197-0.01290.3224-26.1853-54.5984-67.318
230.02180.0109-0.09210.03260.08790.59390.0549-0.02330.08890.17510.2924-0.11130.37310.41420.21560.4665-0.0135-0.44870.2415-0.18880.3928-12.07-69.5153-35.5927
240.16110.0205-0.14020.0211-0.04910.17830.1367-0.06310.03220.05140.0357-0.0895-0.0170.01310.22020.39430.3931-0.08520.3792-0.47430.4773-10.1675-58.8847-57.0446
250.56440.23490.09980.23180.2510.3098-0.05060.06550.1039-0.15790.0509-0.53680.37880.221-0.00110.6113-0.01750.04150.3717-0.04390.5814-8.1923-60.7514-54.8074
260.1211-0.0680.07380.162-0.20990.28560.0417-0.094-0.12880.38270.04-0.07740.5819-0.04920.03031.1622-0.0483-0.11690.2330.00840.4302-20.9354-77.4426-44.2438
271.9901-0.81960.52290.3396-0.21830.13760.07550.18250.5899-0.3859-0.1543-0.0425-0.3743-0.04770.04260.86840.1291-0.17640.3626-0.21510.3894-30.0691-15.0312-69.2387
280.104-0.0097-0.05520.00330.00680.02590.064-0.0040.2984-0.12990.2132-0.1826-0.32930.06320.1840.4891-0.11220.56110.5333-0.08180.6562-28.8879-14.646-63.1896
290.81220.24-0.02470.3412-0.46090.76680.3483-0.33730.27090.21880.18590.1186-0.2189-0.22710.27830.59550.19360.01810.1705-0.0590.3818-38.4765-32.4738-68.7906
300.16010.0382-0.27290.2548-0.17820.49620.13090.4120.1499-0.18890.01350.27170.1618-0.19380.09960.16040.0283-0.09260.2589-0.01570.4265-37.7934-44.6411-64.2729
310.22490.0020.16630.27310.00010.71370.07510.0136-0.08770.08140.1958-0.06870.2707-0.02440.40410.30740.03980.15410.2021-0.10650.1181-32.8234-37.8459-59.8791
320.2212-0.0964-0.28580.26780.32520.58720.0795-0.18930.4717-0.3068-0.2934-0.2888-0.16560.04030.00520.68410.3263-0.00310.70370.070.8532-35.6984-7.3929-62.3731
330.1732-0.2387-0.03121.7618-0.34560.55970.3175-0.09120.2275-0.270.36740.5445-0.5288-0.04820.58270.46460.16540.17720.30190.10760.4365-39.223-32.7587-52.3972
340.2419-0.0257-0.14860.1636-0.09710.22080.1708-0.06580.0381-0.1541-0.01040.1254-0.0293-0.16530.8320.6920.1591-0.23440.4419-0.0901-0.0477-41.5126-32.9852-49.5364
350.16140.03860.09570.23420.06980.0802-0.1007-0.1492-0.12080.0358-0.24110.01750.15-0.1683-0.38990.4185-0.19910.12080.5174-0.05830.3488-41.0197-42.0476-42.2568
360.4080.2290.22790.13760.15950.1963-0.3071-0.18080.1442-0.2513-0.0764-0.1133-0.08430.0882-0.19850.47960.07380.05670.3144-0.04850.5807-41.6233-20.8804-58.3015
370.430.08630.15990.02290.04020.0767-0.16690.07590.5751-0.378-0.07750.0326-0.7262-0.172-0.22390.68330.1523-0.02920.34450.06940.395-38.3159-14.806-73.5384
380.40410.15650.23570.05390.0970.14050.3864-0.2046-0.308-0.06680.0207-0.01080.1461-0.07380.01620.68710.0729-0.11940.3808-0.16610.612237.3441-73.8307-55.5619
390.6273-0.1334-0.22770.05130.02160.3382-0.15820.1433-0.0164-0.1468-0.2558-0.20610.13370.0049-0.36610.28360.3075-0.0010.73860.11710.403846.3913-56.2259-52.2858
400.3137-0.5351-0.08581.6593-0.32660.55730.0935-0.28850.09270.35330.0215-0.6084-0.07240.4297-0.23320.5296-0.08790.13980.4072-0.09030.420441.8846-44.8589-43.6216
410.29760.06270.12740.6821-0.64960.78270.0666-0.0513-0.2118-0.43450.0332-0.14590.51650.3799-0.00270.43540.2239-0.04250.384-0.07240.447638.2167-71.2246-46.9563
420.59170.44510.41960.36470.33540.83590.13150.1266-0.25530.0373-0.1276-0.20930.18560.39720.05280.1745-0.1065-0.10010.80280.1150.091439.0117-58.3516-30.746
430.30490.1767-0.17650.1146-0.13790.2652-0.1550.0552-0.2592-0.1258-0.3536-0.29390.24440.3211-0.37040.22890.10570.14330.48010.09790.595645.4519-69.3728-49.8847
440.1622-0.17870.33040.2225-0.37920.70140.16650.114-0.041-0.14640.1870.07770.07980.00250.60860.2119-0.13320.10720.143-0.21190.531110.3678-24.3335-28.266
452.1394-0.39120.3440.30330.54831.67990.0290.04460.4298-0.17990.25640.012-0.6199-0.2741-0.11760.2803-0.14640.11640.3670.07670.16425.9731-24.0065-40.6221
460.2684-0.05750.12130.15290.02630.0722-0.2469-0.10570.24530.02360.01580.0555-0.4309-0.1193-0.04210.4127-0.0255-0.0880.245-0.05940.31431.551-32.1115-47.7742
470.2238-0.11470.07510.0492-0.02440.02380.14770.0612-0.2549-0.17840.053-0.17140.07240.21060.00630.5118-0.2698-0.05040.5328-0.21320.265231.1654-37.2322-54.0022
480.41060.349-0.51320.4797-0.69581.00630.36290.09670.56230.07050.20410.3995-0.3692-0.28180.53740.19730.0770.01130.3222-0.06760.43235.6803-23.8105-29.2599
490.24340.29720.14920.3770.2510.3793-0.2121-0.03730.0775-0.039-0.03940.3451-0.1305-0.1687-0.10280.4648-0.156-0.02280.33280.04870.358515.6139-34.6183-50.2101
500.61-0.0467-0.29260.50460.2350.46660.1120.19460.1289-0.43790.01940.3076-0.4106-0.14120.00460.6637-0.00670.10880.30540.07440.455811.9618-24.3359-42.4
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 120 )
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 143 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 206 )
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 271 )
9X-RAY DIFFRACTION9chain 'A' and (resid 272 through 335 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 60 )
11X-RAY DIFFRACTION11chain 'B' and (resid 61 through 131 )
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 155 )
13X-RAY DIFFRACTION13chain 'B' and (resid 156 through 189 )
14X-RAY DIFFRACTION14chain 'B' and (resid 190 through 247 )
15X-RAY DIFFRACTION15chain 'B' and (resid 248 through 267 )
16X-RAY DIFFRACTION16chain 'B' and (resid 268 through 313 )
17X-RAY DIFFRACTION17chain 'B' and (resid 314 through 335 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 40 )
19X-RAY DIFFRACTION19chain 'C' and (resid 41 through 60 )
20X-RAY DIFFRACTION20chain 'C' and (resid 61 through 79 )
21X-RAY DIFFRACTION21chain 'C' and (resid 80 through 108 )
22X-RAY DIFFRACTION22chain 'C' and (resid 109 through 142 )
23X-RAY DIFFRACTION23chain 'C' and (resid 143 through 183 )
24X-RAY DIFFRACTION24chain 'C' and (resid 184 through 222 )
25X-RAY DIFFRACTION25chain 'C' and (resid 223 through 304 )
26X-RAY DIFFRACTION26chain 'C' and (resid 305 through 335 )
27X-RAY DIFFRACTION27chain 'D' and (resid 3 through 24 )
28X-RAY DIFFRACTION28chain 'D' and (resid 25 through 44 )
29X-RAY DIFFRACTION29chain 'D' and (resid 45 through 79 )
30X-RAY DIFFRACTION30chain 'D' and (resid 80 through 122 )
31X-RAY DIFFRACTION31chain 'D' and (resid 123 through 156 )
32X-RAY DIFFRACTION32chain 'D' and (resid 157 through 190 )
33X-RAY DIFFRACTION33chain 'D' and (resid 191 through 216 )
34X-RAY DIFFRACTION34chain 'D' and (resid 217 through 247 )
35X-RAY DIFFRACTION35chain 'D' and (resid 248 through 267 )
36X-RAY DIFFRACTION36chain 'D' and (resid 268 through 293 )
37X-RAY DIFFRACTION37chain 'D' and (resid 294 through 335 )
38X-RAY DIFFRACTION38chain 'E' and (resid 3 through 46 )
39X-RAY DIFFRACTION39chain 'E' and (resid 47 through 79 )
40X-RAY DIFFRACTION40chain 'E' and (resid 80 through 142 )
41X-RAY DIFFRACTION41chain 'E' and (resid 143 through 216 )
42X-RAY DIFFRACTION42chain 'E' and (resid 217 through 259 )
43X-RAY DIFFRACTION43chain 'E' and (resid 260 through 335 )
44X-RAY DIFFRACTION44chain 'F' and (resid 3 through 46 )
45X-RAY DIFFRACTION45chain 'F' and (resid 47 through 80 )
46X-RAY DIFFRACTION46chain 'F' and (resid 81 through 120 )
47X-RAY DIFFRACTION47chain 'F' and (resid 121 through 142 )
48X-RAY DIFFRACTION48chain 'F' and (resid 143 through 188 )
49X-RAY DIFFRACTION49chain 'F' and (resid 189 through 239 )
50X-RAY DIFFRACTION50chain 'F' and (resid 240 through 335 )

+
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