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- PDB-5v7g: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

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Basic information

Entry
Database: PDB / ID: 5v7g
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADPH and oxalate
ComponentsNADPH-dependent glyoxylate/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / NADPH-dependent glyoxylate/hydroxypyruvate reductase / NADP / NYSGRC / Sinorhizobium meliloti / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / metal ion binding / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / OXALATE ION / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsShabalin, I.G. / Mason, D.V. / Handing, K.B. / Kutner, J. / Matelska, D. / Cooper, D.R. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117080 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HG008424 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Authors: Kutner, J. / Shabalin, I.G. / Matelska, D. / Handing, K.B. / Gasiorowska, O. / Sroka, P. / Gorna, M.W. / Ginalski, K. / Wozniak, K. / Minor, W.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 16, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_ec
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27823
Polymers137,4344
Non-polymers3,84419
Water32,4631802
1
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,68512
Polymers68,7172
Non-polymers1,96810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-86 kcal/mol
Surface area23700 Å2
MethodPISA
2
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,59311
Polymers68,7172
Non-polymers1,8769
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-84 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.209, 178.209, 133.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 319 / Label seq-ID: 4 - 320

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NADPH-dependent glyoxylate/hydroxypyruvate reductase / 2-hydroxyacid dehydrogenase


Mass: 34358.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc04462 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q92LZ4, hydroxypyruvate reductase

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Non-polymers , 6 types, 1821 molecules

#2: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1802 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADPH, 50 mM oxalic acid, pH 7.0 + 0.2 uL TOP96 condition #41 (0.1 ...Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADPH, 50 mM oxalic acid, pH 7.0 + 0.2 uL TOP96 condition #41 (0.1 M sodium cacodylate, pH 6.5, 18% w/v PEG8000, 0.2 M sodium acetate), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/20 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2015 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.301
11K, H, -L20.699
ReflectionResolution: 1.75→50 Å / Num. obs: 157652 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.043 / Rrim(I) all: 0.092 / Rsym value: 0.081 / Χ2: 1.526 / Net I/av σ(I): 17.9 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.75-1.784.30.6672.1795879580.7830.3590.760.6670.84499.7
1.78-1.814.60.580.8430.3020.6560.866100
1.81-1.854.60.4920.8790.2550.5550.90499.9
1.85-1.894.60.4080.8960.2110.4610.98999.9
1.89-1.934.60.3490.9160.1810.3941.25899.9
1.93-1.974.60.2850.9520.1480.3221.213100
1.97-2.024.70.2330.9630.1210.2631.21199.9
2.02-2.074.60.2090.9710.1090.2361.4899.9
2.07-2.144.70.1730.9780.090.1961.529100
2.14-2.24.70.150.9820.0780.1691.695100
2.2-2.284.70.1520.9810.0790.1721.999100
2.28-2.384.80.1280.9850.0670.1451.742100
2.38-2.484.70.1190.9870.0620.1341.873100
2.48-2.614.70.1070.9880.0560.1212.057100
2.61-2.784.60.0980.990.0520.1111.96199.8
2.78-2.994.50.0840.9920.0450.0962.02399.6
2.99-3.294.40.0710.9940.0380.0811.92398.7
3.29-3.774.10.060.9960.0330.0691.74295.9
3.77-4.7540.050.9970.0270.0571.60692.2
4.75-5040.0470.9960.0260.0541.63291.2

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5J23
Resolution: 1.75→37.07 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.396 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.019 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1801 7896 5 %RANDOM
Rwork0.1498 ---
obs0.1514 149734 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.32 Å2 / Biso mean: 31.43 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1--4.97 Å2-0 Å2-0 Å2
2---4.97 Å2-0 Å2
3---9.95 Å2
Refinement stepCycle: final / Resolution: 1.75→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9429 0 242 1804 11475
Biso mean--26.77 41.02 -
Num. residues----1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199888
X-RAY DIFFRACTIONr_bond_other_d0.0020.029549
X-RAY DIFFRACTIONr_angle_refined_deg1.462.00813506
X-RAY DIFFRACTIONr_angle_other_deg0.969321921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78851266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06122.452363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.592151499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0121597
X-RAY DIFFRACTIONr_chiral_restr0.0790.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021973
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A196260.04
12B196260.04
21A197080.03
22C197080.03
31A196280.04
32D196280.04
41B196980.04
42C196980.04
51B198380.03
52D198380.03
61C196900.04
62D196900.04
LS refinement shellResolution: 1.751→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 548 -
Rwork0.176 11200 -
all-11748 -
obs--99.63 %
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)
13.40261.2608-0.30754.88710.3594.32360.0266-0.0168-0.1888-0.0914-0.019-0.22490.14480.2286-0.00750.11480.0381-0.07480.12220.0040.145966.01815.32520.828
23.2244-0.3757-2.22562.48930.04072.26310.02710.0929-0.1852-0.36030.0267-0.36590.17870.3589-0.05380.20.0505-0.06870.2834-0.09440.248568.29415.0698.461
30.46560.35730.17471.49910.44290.47280.05230.04430.002-0.128-0.0030.0298-0.0827-0.0456-0.04940.09450.005-0.00690.0959-0.00320.075161.16543.81519.295
48.1206-1.3113-5.97023.38196.251315.37970.1783-0.12360.507-0.0253-0.30670.5275-0.3602-1.12040.12850.34420.05780.05670.32430.04320.424742.90844.7739.471
50.56090.2610.07461.29620.08110.53670.01540.10440.018-0.23810.01590.0227-0.07660.0007-0.03140.1240.0141-0.02170.1117-0.01260.060361.34840.32311.851
62.4477-1.26440.12054.70960.08022.2660.0490.01250.16740.00860.0043-0.1882-0.16060.1665-0.05330.1272-0.03050.06470.1491-0.00390.16567.76484.0632.631
71.9194-0.09630.65840.6254-0.13821.4260.0384-0.06470.08460.12660.0079-0.38380.00890.4813-0.04640.1909-0.04090.03460.2892-0.09270.331971.5883.79545.25
80.481-0.5567-0.27141.57810.56570.49580.0438-0.07070.04510.08870.01610.03460.0454-0.0408-0.05980.0872-0.01010.00990.1112-0.00940.069562.04654.11634.895
91.47990.1722-0.53853.67010.87721.08330.0249-0.15730.04540.2562-0.02090.37240.0198-0.2802-0.0040.18720.01040.04450.23610.01360.116152.06652.18547.493
100.56-0.2792-0.24451.64680.26730.4514-0.0019-0.15720.04330.2120.0791-0.12210.04830.0517-0.07730.1147-0.01950.01050.1273-0.03080.07664.68260.90942.06
115.3088-2.82593.03826.3231-2.55546.21740.0109-0.1146-0.08570.08580.06550.33030.0185-0.2805-0.07630.0555-0.04370.04790.12230.0330.1149-18.72337.80342.817
122.54780.14370.43782.54260.09162.95120.03610.1467-0.115-0.11430.01750.33120.2358-0.4248-0.05370.0801-0.02020.01060.12140.06640.1572-21.37637.35838.614
131.0577-0.76020.34311.1317-0.47270.49980.06260.1273-0.0157-0.05040.00180.05210.01640.0463-0.06440.0483-0.00550.00430.05160.00430.04644.4928.341.345
143.1113-0.91920.38732.1948-0.80881.86330.01990.23810.2879-0.0596-0.0471-0.2346-0.23740.26520.02710.108-0.00570.03010.13160.02930.084416.86734.07831.408
150.9562-0.38630.13890.9597-0.31840.62490.05750.1746-0.046-0.1127-0.02050.0320.08320.0397-0.0370.0511-0.0062-0.00450.07880.01340.04081.53929.09835.665
164.7402-0.0831-0.69621.7558-0.37222.4470.0258-0.08-0.27020.03710.0426-0.06690.27850.0575-0.06850.14190.0082-0.04840.0649-0.0550.141838.8051.92855.662
171.79750.8272-0.26673.1193-0.30461.2174-0.0235-0.1957-0.40710.20180.03660.18420.3657-0.1529-0.0130.2291-0.0053-0.04820.1584-0.00660.218535.361-2.75566.514
181.5546-0.24880.57120.2306-0.03590.45740.0704-0.1091-0.12470.09450.0361-0.03020.0464-0.0269-0.10660.0784-0.0112-0.02170.0359-0.00090.06118.55517.97359.454
190.5211-0.35850.60370.82850.0893.7035-0.0585-0.06540.24740.1340.0511-0.1715-0.36850.15570.00740.1678-0.0122-0.00740.1264-0.0420.176218.95635.40466.298
201.7688-0.41320.34170.52440.07410.4683-0.0121-0.239-0.11010.13990.05770.02330.0291-0.0777-0.04560.10360.0025-0.02640.05610.01020.062420.18217.20165.251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 31
2X-RAY DIFFRACTION2A32 - 61
3X-RAY DIFFRACTION3A62 - 172
4X-RAY DIFFRACTION4A173 - 180
5X-RAY DIFFRACTION5A181 - 319
6X-RAY DIFFRACTION6B3 - 26
7X-RAY DIFFRACTION7B27 - 66
8X-RAY DIFFRACTION8B67 - 170
9X-RAY DIFFRACTION9B171 - 207
10X-RAY DIFFRACTION10B208 - 319
11X-RAY DIFFRACTION11C3 - 15
12X-RAY DIFFRACTION12C16 - 52
13X-RAY DIFFRACTION13C53 - 165
14X-RAY DIFFRACTION14C166 - 207
15X-RAY DIFFRACTION15C208 - 319
16X-RAY DIFFRACTION16D3 - 27
17X-RAY DIFFRACTION17D28 - 53
18X-RAY DIFFRACTION18D54 - 158
19X-RAY DIFFRACTION19D159 - 194
20X-RAY DIFFRACTION20D195 - 319

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