[English] 日本語
Yorodumi
- PDB-5nue: Cytosolic Malate Dehydrogenase 1 (peroxide-treated) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nue
TitleCytosolic Malate Dehydrogenase 1 (peroxide-treated)
Components(Malate dehydrogenase 1, ...) x 3
KeywordsOXIDOREDUCTASE / Dehydrogenase / Oxidized / Malate/Oxaloacetate / NAD+
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / plasmodesma / plant-type vacuole / oxaloacetate metabolic process / apoplast / NADH metabolic process / chloroplast stroma / response to zinc ion ...malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / plasmodesma / plant-type vacuole / oxaloacetate metabolic process / apoplast / NADH metabolic process / chloroplast stroma / response to zinc ion / tricarboxylic acid cycle / chloroplast / mRNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain ...Malate dehydrogenase, NAD-dependent, cytosolic / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-ETHOXYETHANOL / FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / HYDROGEN PEROXIDE / Malate dehydrogenase 1, cytoplasmic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35000279615 Å
AuthorsYoung, D. / Messens, J. / Huang, J. / Reichheld, J.-P.
Funding support France, Belgium, 4items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique and the Agence Nationale de la RechercheANR-Blanc Cynthiol 12-BSV6-0011 France
VIB Belgium
Vrije Universiteit BrusselSPR34 Belgium
Research Foundation Flanders (FWO) Belgium
CitationJournal: J. Exp. Bot. / Year: 2018
Title: Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis.
Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / ...Authors: Huang, J. / Niazi, A.K. / Young, D. / Rosado, L.A. / Vertommen, D. / Bodra, N. / Abdelgawwad, M.R. / Vignols, F. / Wei, B. / Wahni, K. / Bashandy, T. / Bariat, L. / Van Breusegem, F. / Messens, J. / Reichheld, J.P.
History
DepositionApr 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
C: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,42044
Polymers106,9293
Non-polymers4,49141
Water17,997999
1
A: Malate dehydrogenase 1, cytoplasmic
B: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,44331
Polymers71,2862
Non-polymers3,15729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-103 kcal/mol
Surface area24100 Å2
MethodPISA
2
C: Malate dehydrogenase 1, cytoplasmic
hetero molecules

C: Malate dehydrogenase 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,95426
Polymers71,2862
Non-polymers2,66824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area10220 Å2
ΔGint-110 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.598, 118.374, 148.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-797-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 2 through 3 or resid 6...A2 - 3
121(chain 'A' and (resid 2 through 3 or resid 6...A6 - 14
131(chain 'A' and (resid 2 through 3 or resid 6...A17 - 23
141(chain 'A' and (resid 2 through 3 or resid 6...A25
151(chain 'A' and (resid 2 through 3 or resid 6...A30 - 32
161(chain 'A' and (resid 2 through 3 or resid 6...A35 - 40
171(chain 'A' and (resid 2 through 3 or resid 6...A42 - 47
181(chain 'A' and (resid 2 through 3 or resid 6...A50 - 51
191(chain 'A' and (resid 2 through 3 or resid 6...A53 - 55
1101(chain 'A' and (resid 2 through 3 or resid 6...A57 - 58
1111(chain 'A' and (resid 2 through 3 or resid 6...A60 - 86
1121(chain 'A' and (resid 2 through 3 or resid 6...A88 - 93
1131(chain 'A' and (resid 2 through 3 or resid 6...A95
1141(chain 'A' and (resid 2 through 3 or resid 6...A98 - 102
1151(chain 'A' and (resid 2 through 3 or resid 6...A105 - 107
1161(chain 'A' and (resid 2 through 3 or resid 6...A109 - 117
1171(chain 'A' and (resid 2 through 3 or resid 6...A120 - 121
1181(chain 'A' and (resid 2 through 3 or resid 6...A125
1191(chain 'A' and (resid 2 through 3 or resid 6...A127 - 132
1201(chain 'A' and (resid 2 through 3 or resid 6...A134 - 140
1211(chain 'A' and (resid 2 through 3 or resid 6...A143 - 146
1221(chain 'A' and (resid 2 through 3 or resid 6...A148 - 149
1231(chain 'A' and (resid 2 through 3 or resid 6...A152 - 167
1241(chain 'A' and (resid 2 through 3 or resid 6...A170 - 189
1251(chain 'A' and (resid 2 through 3 or resid 6...A191 - 197
1261(chain 'A' and (resid 2 through 3 or resid 6...A199 - 208
1271(chain 'A' and (resid 2 through 3 or resid 6...A210 - 221
1281(chain 'A' and (resid 2 through 3 or resid 6...A224 - 225
1291(chain 'A' and (resid 2 through 3 or resid 6...A227 - 235
1301(chain 'A' and (resid 2 through 3 or resid 6...A237 - 239
1311(chain 'A' and (resid 2 through 3 or resid 6...A246 - 247
1321(chain 'A' and (resid 2 through 3 or resid 6...A251 - 255
1331(chain 'A' and (resid 2 through 3 or resid 6...A257 - 273
1341(chain 'A' and (resid 2 through 3 or resid 6...A275 - 281
1351(chain 'A' and (resid 2 through 3 or resid 6...A283 - 294
1361(chain 'A' and (resid 2 through 3 or resid 6...A297
1371(chain 'A' and (resid 2 through 3 or resid 6...A299 - 306
1381(chain 'A' and (resid 2 through 3 or resid 6...A308 - 310
1391(chain 'A' and (resid 2 through 3 or resid 6...A312 - 316
1401(chain 'A' and (resid 2 through 3 or resid 6...A319 - 320
1411(chain 'A' and (resid 2 through 3 or resid 6...A323 - 324
1421(chain 'A' and (resid 2 through 3 or resid 6...A326
1431(chain 'A' and (resid 2 through 3 or resid 6...A332
2441(chain 'B' and (resid 2 through 3 or resid 6...B2 - 3
2451(chain 'B' and (resid 2 through 3 or resid 6...B6 - 14
2461(chain 'B' and (resid 2 through 3 or resid 6...B17 - 23
2471(chain 'B' and (resid 2 through 3 or resid 6...B25
2481(chain 'B' and (resid 2 through 3 or resid 6...B30 - 32
2491(chain 'B' and (resid 2 through 3 or resid 6...B35 - 40
2501(chain 'B' and (resid 2 through 3 or resid 6...B42 - 47
2511(chain 'B' and (resid 2 through 3 or resid 6...B50 - 51
2521(chain 'B' and (resid 2 through 3 or resid 6...B53 - 55
2531(chain 'B' and (resid 2 through 3 or resid 6...B57 - 58
2541(chain 'B' and (resid 2 through 3 or resid 6...B60 - 86
2551(chain 'B' and (resid 2 through 3 or resid 6...B88 - 93
2561(chain 'B' and (resid 2 through 3 or resid 6...B95
2571(chain 'B' and (resid 2 through 3 or resid 6...B98 - 102
2581(chain 'B' and (resid 2 through 3 or resid 6...B105 - 107
2591(chain 'B' and (resid 2 through 3 or resid 6...B109 - 117
2601(chain 'B' and (resid 2 through 3 or resid 6...B120 - 121
2611(chain 'B' and (resid 2 through 3 or resid 6...B125
2621(chain 'B' and (resid 2 through 3 or resid 6...B127 - 132
2631(chain 'B' and (resid 2 through 3 or resid 6...B134 - 140
2641(chain 'B' and (resid 2 through 3 or resid 6...B143 - 146
2651(chain 'B' and (resid 2 through 3 or resid 6...B148 - 149
2661(chain 'B' and (resid 2 through 3 or resid 6...B152 - 167
2671(chain 'B' and (resid 2 through 3 or resid 6...B170 - 189
2681(chain 'B' and (resid 2 through 3 or resid 6...B191 - 197
2691(chain 'B' and (resid 2 through 3 or resid 6...B199 - 208
2701(chain 'B' and (resid 2 through 3 or resid 6...B210 - 221
2711(chain 'B' and (resid 2 through 3 or resid 6...B224 - 225
2721(chain 'B' and (resid 2 through 3 or resid 6...B227 - 235
2731(chain 'B' and (resid 2 through 3 or resid 6...B237 - 239
2741(chain 'B' and (resid 2 through 3 or resid 6...B246 - 247
2751(chain 'B' and (resid 2 through 3 or resid 6...B251 - 255
2761(chain 'B' and (resid 2 through 3 or resid 6...B257 - 273
2771(chain 'B' and (resid 2 through 3 or resid 6...B275 - 281
2781(chain 'B' and (resid 2 through 3 or resid 6...B283 - 294
2791(chain 'B' and (resid 2 through 3 or resid 6...B297
2801(chain 'B' and (resid 2 through 3 or resid 6...B299 - 306
2811(chain 'B' and (resid 2 through 3 or resid 6...B308 - 310
2821(chain 'B' and (resid 2 through 3 or resid 6...B312 - 316
2831(chain 'B' and (resid 2 through 3 or resid 6...B319 - 320
2841(chain 'B' and (resid 2 through 3 or resid 6...B323 - 324
2851(chain 'B' and (resid 2 through 3 or resid 6...B326
2861(chain 'B' and (resid 2 through 3 or resid 6...B332
3871(chain 'C' and (resid 2 through 3 or resid 6...C2 - 3
3881(chain 'C' and (resid 2 through 3 or resid 6...C6 - 14
3891(chain 'C' and (resid 2 through 3 or resid 6...C17 - 23
3901(chain 'C' and (resid 2 through 3 or resid 6...C25
3911(chain 'C' and (resid 2 through 3 or resid 6...C30 - 32
3921(chain 'C' and (resid 2 through 3 or resid 6...C35 - 40
3931(chain 'C' and (resid 2 through 3 or resid 6...C42 - 47
3941(chain 'C' and (resid 2 through 3 or resid 6...C50 - 51
3951(chain 'C' and (resid 2 through 3 or resid 6...C53 - 55
3961(chain 'C' and (resid 2 through 3 or resid 6...C57 - 58
3971(chain 'C' and (resid 2 through 3 or resid 6...C60 - 86
3981(chain 'C' and (resid 2 through 3 or resid 6...C88 - 93
3991(chain 'C' and (resid 2 through 3 or resid 6...C95
31001(chain 'C' and (resid 2 through 3 or resid 6...C98 - 102
31011(chain 'C' and (resid 2 through 3 or resid 6...C105 - 107
31021(chain 'C' and (resid 2 through 3 or resid 6...C109 - 117
31031(chain 'C' and (resid 2 through 3 or resid 6...C120 - 121
31041(chain 'C' and (resid 2 through 3 or resid 6...C125
31051(chain 'C' and (resid 2 through 3 or resid 6...C127 - 132
31061(chain 'C' and (resid 2 through 3 or resid 6...C134 - 140
31071(chain 'C' and (resid 2 through 3 or resid 6...C143 - 146
31081(chain 'C' and (resid 2 through 3 or resid 6...C148 - 149
31091(chain 'C' and (resid 2 through 3 or resid 6...C152 - 167
31101(chain 'C' and (resid 2 through 3 or resid 6...C170 - 189
31111(chain 'C' and (resid 2 through 3 or resid 6...C191 - 197
31121(chain 'C' and (resid 2 through 3 or resid 6...C199 - 208
31131(chain 'C' and (resid 2 through 3 or resid 6...C210 - 221
31141(chain 'C' and (resid 2 through 3 or resid 6...C224 - 225
31151(chain 'C' and (resid 2 through 3 or resid 6...C227 - 235
31161(chain 'C' and (resid 2 through 3 or resid 6...C237 - 239
31171(chain 'C' and (resid 2 through 3 or resid 6...C246 - 247
31181(chain 'C' and (resid 2 through 3 or resid 6...C251 - 255
31191(chain 'C' and (resid 2 through 3 or resid 6...C257 - 273
31201(chain 'C' and (resid 2 through 3 or resid 6...C275 - 281
31211(chain 'C' and (resid 2 through 3 or resid 6...C283 - 294
31221(chain 'C' and (resid 2 through 3 or resid 6...C297
31231(chain 'C' and (resid 2 through 3 or resid 6...C299 - 306
31241(chain 'C' and (resid 2 through 3 or resid 6...C308 - 310
31251(chain 'C' and (resid 2 through 3 or resid 6...C312 - 316
31261(chain 'C' and (resid 2 through 3 or resid 6...C319 - 320
31271(chain 'C' and (resid 2 through 3 or resid 6...C323 - 324
31281(chain 'C' and (resid 2 through 3 or resid 6...C326
31291(chain 'C' and (resid 2 through 3 or resid 6...C332

-
Components

-
Malate dehydrogenase 1, ... , 3 types, 3 molecules ABC

#1: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35610.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 56 oxidized to methionine sulfoxide / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cell: cytoplasmic / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase
#2: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35674.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase
#3: Protein Malate dehydrogenase 1, cytoplasmic / Cytosolic NAD-dependent malate dehydrogenase 1 / cNAD-MDH1 / Cytosolic malate dehydrogenase 1 / Cytosolic MDH1


Mass: 35642.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MDH1, At1g04410, F19P19.13 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P93819, malate dehydrogenase

-
Non-polymers , 10 types, 1040 molecules

#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: H2O2
#8: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#11: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.66 Å3/Da / Density % sol: 53.87 % / Description: 100 um x 200 um
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M ammonium sulfate, 0.1 M Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980105 Å / Relative weight: 1
ReflectionResolution: 1.35→92.561 Å / Num. obs: 236503 / % possible obs: 99.96 % / Redundancy: 13.6 % / Biso Wilson estimate: 14.47098422 Å2 / CC1/2: 0.973 / Rrim(I) all: 0.1092 / Net I/σ(I): 5.56
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 0.63 / CC1/2: 0.369 / Rpim(I) all: 0.798 / Rrim(I) all: 2.934 / % possible all: 99.98

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35000279615→92.5612886735 Å / SU ML: 0.163547634761 / Cross valid method: FREE R-VALUE / σ(F): 1.32522207677 / Phase error: 19.3646044324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.179506294341 12401 4.98260247664 %
Rwork0.146297730068 236485 -
obs0.147967919778 248886 99.9213110542 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.3464790462 Å2
Refinement stepCycle: LAST / Resolution: 1.35000279615→92.5612886735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7454 0 283 999 8736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01378131529378471
X-RAY DIFFRACTIONf_angle_d1.4132965480611621
X-RAY DIFFRACTIONf_chiral_restr0.1024878580111341
X-RAY DIFFRACTIONf_plane_restr0.008548986203171483
X-RAY DIFFRACTIONf_dihedral_angle_d15.69489762423326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.3534770925484150.3291972311787742X-RAY DIFFRACTION99.6335654086
1.3653-1.38140.339133700014080.3111337641647777X-RAY DIFFRACTION99.7805680848
1.3814-1.39830.3417938762344120.3046699052527811X-RAY DIFFRACTION99.85428051
1.3983-1.4160.325571749513890.2852612478167826X-RAY DIFFRACTION99.8905642023
1.416-1.43460.3050356264344150.2626751673757872X-RAY DIFFRACTION99.8794745089
1.4346-1.45420.2784718902753900.2602562091797800X-RAY DIFFRACTION99.9633833761
1.4542-1.4750.2851640907243810.2482736482397857X-RAY DIFFRACTION99.9757281553
1.475-1.4970.2758027369814330.2363601775527818X-RAY DIFFRACTION99.9515445185
1.497-1.52040.2515531752233900.2165036185477801X-RAY DIFFRACTION99.9755889174
1.5204-1.54540.2648958041624350.2046022239747852X-RAY DIFFRACTION99.951754915
1.5454-1.5720.2484226737174160.1859796234917813X-RAY DIFFRACTION99.9757016158
1.572-1.60060.2161076683233970.1734826857787819X-RAY DIFFRACTION99.9878301083
1.6006-1.63140.200034286044110.1577038243947841X-RAY DIFFRACTION99.9515503876
1.6314-1.66470.1973767772144290.1462218940467876X-RAY DIFFRACTION99.9879605105
1.6647-1.70090.1747291159474150.1348923662117851X-RAY DIFFRACTION100
1.7009-1.74050.1796108941563810.1360017267827868X-RAY DIFFRACTION100
1.7405-1.7840.1779721533774170.1323359713697814X-RAY DIFFRACTION99.9878522838
1.784-1.83220.1713084797434230.1227106829357876X-RAY DIFFRACTION99.9518246417
1.8322-1.88620.1694879965764290.1265625392667852X-RAY DIFFRACTION99.9879256218
1.8862-1.9470.1717449970824110.1198035490517901X-RAY DIFFRACTION99.9639206254
1.947-2.01660.1719795709834260.1166444075377866X-RAY DIFFRACTION99.9397372544
2.0166-2.09740.1565889588913510.1169523567557918X-RAY DIFFRACTION99.9516499456
2.0974-2.19280.1659888234334200.1177319754427893X-RAY DIFFRACTION99.8798510153
2.1928-2.30850.1524234808864290.1170493241047913X-RAY DIFFRACTION99.8205097523
2.3085-2.45310.1567714613664290.1244260278647891X-RAY DIFFRACTION99.8559769563
2.4531-2.64250.1708446256533910.1292599695317965X-RAY DIFFRACTION99.8446648345
2.6425-2.90850.1622258972684330.1372893544597953X-RAY DIFFRACTION99.9046938289
2.9085-3.32930.1564872556534520.1399840800287957X-RAY DIFFRACTION99.9049542592
3.3293-4.19460.1413581099994460.1236298504628074X-RAY DIFFRACTION99.9882642882
4.1946-92.77960.1657369744234270.1445080789138388X-RAY DIFFRACTION99.9206529132

+
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://pdbjlvh1.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