[English] 日本語
Yorodumi
- PDB-5j23: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j23
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose
Components2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / 2-hydroxyacid dehydrogenase / NADP / NYSGRC / 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-A2R / ACETATE ION / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShabalin, I.G. / Gasiorowska, O.A. / Handing, K.B. / Bonanno, J. / Kutner, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.4May 23, 2018Group: Data collection / Experimental preparation / Structure summary
Category: exptl_crystal_grow / struct / Item: _exptl_crystal_grow.pdbx_details / _struct.title
Revision 1.5Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Sep 27, 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.beg_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-hydroxyacid dehydrogenase
B: 2-hydroxyacid dehydrogenase
C: 2-hydroxyacid dehydrogenase
D: 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,41618
Polymers137,4344
Non-polymers2,98214
Water10,863603
1
A: 2-hydroxyacid dehydrogenase
C: 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2209
Polymers68,7172
Non-polymers1,5037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-63 kcal/mol
Surface area24230 Å2
MethodPISA
2
B: 2-hydroxyacid dehydrogenase
D: 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1969
Polymers68,7172
Non-polymers1,4797
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-75 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.822, 175.822, 136.839
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: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 3 - 320 / Label seq-ID: 4 - 321

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

-
Components

#1: Protein
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 (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92LZ4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-A2R / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 639.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N5O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 13 mg/ml protein in 10 mM NADPH, 10 mM Glycolic Acid, 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 ...Details: 0.2 ul of 13 mg/ml protein in 10 mM NADPH, 10 mM Glycolic Acid, 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 2 condition #20 (1.1 M Malonic acid, 0.072 M Succinic acid, 0.15M Ammonium dihydrogen citrate, 0.18 M DL-Malic Acid, 0.096 M Ammonium tartrate, 0.24 M Sodium acetate anhydrous, 0.3 M Sodium formate, pH=7.0) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours.

-
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: Nov 6, 2014 / 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, L10.237
11K, H, -L20.763
ReflectionResolution: 2.3→50 Å / Num. obs: 70083 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/av σ(I): 18.22 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.343.90.6621.81100
2.34-2.383.90.6041100
2.38-2.433.90.5181100
2.43-2.483.90.4341100
2.48-2.533.90.381100
2.53-2.593.90.3621100
2.59-2.663.90.3051100
2.66-2.733.90.2531100
2.73-2.813.90.21100
2.81-2.93.90.1611100
2.9-33.90.1381100
3-3.123.90.1111100
3.12-3.263.90.091100
3.26-3.443.90.0761100
3.44-3.653.90.0641100
3.65-3.933.90.055199.9
3.93-4.333.90.0511100
4.33-4.953.90.0431100
4.95-6.243.90.0421100
6.24-503.80.03199.7

-
Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0P

4z0p


Resolution: 2.3→36.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 6.243 / SU ML: 0.087 / SU R Cruickshank DPI: 0.0458 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.033
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3434 4.9 %RANDOM
Rwork0.1464 ---
obs0.1475 66631 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.08 Å2 / Biso mean: 46.78 Å2 / Biso min: 25.13 Å2
Baniso -1Baniso -2Baniso -3
1--8.99 Å2-0 Å2-0 Å2
2---8.99 Å2-0 Å2
3---17.99 Å2
Refinement stepCycle: final / Resolution: 2.3→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9454 0 179 603 10236
Biso mean--52.04 46.2 -
Num. residues----1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199807
X-RAY DIFFRACTIONr_bond_other_d0.0070.029675
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.98513430
X-RAY DIFFRACTIONr_angle_other_deg1.21322102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43751268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24122.256359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.775151493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5541599
X-RAY DIFFRACTIONr_chiral_restr0.0830.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111179
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022116
X-RAY DIFFRACTIONr_mcbond_it1.2932.6845087
X-RAY DIFFRACTIONr_mcbond_other1.2812.6825083
X-RAY DIFFRACTIONr_mcangle_it2.024.026348
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A393820.02
12B393820.02
21A391860.04
22C391860.04
31A391300.05
32D391300.05
41B390920.04
42C390920.04
51B388660.05
52D388660.05
61C392320.04
62D392320.04
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 256 -
Rwork0.22 4910 -
all-5166 -
obs--99.02 %
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)
11.4573-0.0286-0.36433.79661.59334.01850.05490.01220.27360.08330.07390.3944-0.2932-0.4217-0.12880.15190.0681-0.00360.21190.16110.2406-19.5170.22987.151
21.00760.1453-0.27944.95421.4746.13670.1677-0.28660.34270.3076-0.02930.2413-0.3871-0.2238-0.13830.23790.05640.02810.28060.04260.3276-17.16970.23497.402
32.0761.6464-0.91651.9375-0.89650.610.1015-0.1570.04090.06060.01950.0602-0.02470.0451-0.1210.13570.02990.02630.09640.03280.0887.88778.38286.11
42.82911.0134-0.0072.49750.13213.62840.2258-0.8004-0.46940.5913-0.2123-0.13650.34750.252-0.01360.2724-0.0099-0.04610.33690.15280.211117.81971.69395.92
53.58811.6510.84172.49490.11371.91010.2296-0.6710.40080.4525-0.2260.1475-0.21570.0077-0.00360.1699-0.02240.08980.2474-0.0210.12889.15885.45392.174
61.52790.5285-1.04642.8108-1.02323.8728-0.11030.019-0.14380.00970.12910.06740.2481-0.2052-0.01890.1024-0.012-0.01810.11670.09210.1753-9.90557.95290.7
72.6456-0.2992-0.24191.95960.59652.3490.0527-0.21190.0866-0.01050.1409-0.296-0.09710.6141-0.19360.1256-0.04820.11870.2556-0.10870.175168.60981.311109.77
80.1225-0.29130.04673.13160.99520.70730.0441-0.04970.02010.10580.1089-0.06290.06980.0513-0.15310.0627-0.01560.0320.1504-0.06030.138164.54151.306103.453
94.39021.17181.061910.25882.38015.63510.0389-0.31950.16560.3402-0.10620.8041-0.1725-0.39950.06720.1069-0.00990.05920.1997-0.01720.17250.43351.431104.655
107.9633-0.4346-2.74015.8540.27543.8134-0.113-0.57620.49960.91950.16140.6012-0.2038-0.3224-0.04830.29590.02510.06380.3194-0.05640.184250.64849.079116.713
113.8516-0.52420.92832.8662-0.22683.653-0.2132-0.79730.22110.9340.1584-0.2043-0.0888-0.09880.05470.3520.0378-0.03910.2926-0.10030.141965.35446.752118.078
121.0265-1.5818-0.68854.5761.54251.041-0.0284-0.20170.07820.28670.1888-0.2990.03950.1064-0.16050.0771-0.04960.01990.1235-0.06220.134862.82768.11108.518
134.5276-0.553-0.60435.1604-0.30025.23010.02620.07550.5755-0.01990.0261-0.2207-0.5540.1482-0.05230.1663-0.01340.05730.1229-0.0740.220443.521101.4968.581
143.3120.9933-0.79470.4868-0.24340.58170.01280.16630.1494-0.11690.1108-0.00510.0032-0.0259-0.12360.13810.02510.03770.0942-0.00510.113323.44986.33468.377
152.96540.8203-0.67822.87420.85975.71850.06310.4062-0.5513-0.46340.0887-0.47290.48990.3117-0.15190.32130.06190.11230.2014-0.07510.266621.06768.31163.677
164.45970.10770.79123.26860.47154.0372-0.06130.79670.0233-0.72010.0276-0.1701-0.06820.19550.03360.30720.00370.09120.27380.0420.123715.40380.8957.29
174.14191.00970.07740.75790.10660.5896-0.00620.27810.2623-0.24990.11230.1285-0.051-0.0417-0.10620.19750.00650.04320.11070.02650.13720.95388.77967.642
181.9142-1.15070.20022.47661.58786.4163-0.0046-0.0284-0.1537-0.01720.1041-0.2950.00170.3026-0.09940.1110.01150.05490.1465-0.00270.208350.47685.00162.473
193.3391-0.7849-0.45484.39320.61444.3316-0.088-0.1756-0.10160.06330.1206-0.30690.23480.3891-0.03270.15490.0311-0.09440.1522-0.00470.137666.89613.45487.317
200.42430.7980.27543.18781.16120.6213-0.01060.0678-0.0421-0.2510.1505-0.07010.03260.0858-0.13990.1225-0.0061-0.06830.1073-0.02650.090860.91828.3483.28
216.35482.81151.12389.4379-4.60583.3944-0.23980.15820.31090.1666-0.4727-0.9951-0.17280.37980.71260.1715-0.03-0.06480.2558-0.13970.519178.96657.85102.47
221.35990.89711.26333.03630.28742.33560.13270.11860.0461-0.45490.06090.59170.0747-0.3532-0.19360.1990.0381-0.08310.3142-0.01510.232350.8349.92584.502
231.51880.01120.22123.1021-0.78652.24150.04370.41770.0868-0.67290.0123-0.21840.01110.1409-0.0560.20560.00690.03350.2166-0.06990.119565.60146.68480.365
242.16140.79081.42552.99042.27863.79690.1039-0.0886-0.20390.086-0.07390.15520.3445-0.2018-0.02990.1293-0.0029-0.06890.0844-0.0170.090351.71617.45285.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 41
2X-RAY DIFFRACTION2A42 - 61
3X-RAY DIFFRACTION3A62 - 151
4X-RAY DIFFRACTION4A152 - 219
5X-RAY DIFFRACTION5A220 - 286
6X-RAY DIFFRACTION6A287 - 320
7X-RAY DIFFRACTION7B3 - 75
8X-RAY DIFFRACTION8B76 - 149
9X-RAY DIFFRACTION9B150 - 167
10X-RAY DIFFRACTION10B168 - 203
11X-RAY DIFFRACTION11B204 - 252
12X-RAY DIFFRACTION12B253 - 320
13X-RAY DIFFRACTION13C3 - 43
14X-RAY DIFFRACTION14C44 - 151
15X-RAY DIFFRACTION15C152 - 197
16X-RAY DIFFRACTION16C198 - 243
17X-RAY DIFFRACTION17C244 - 298
18X-RAY DIFFRACTION18C299 - 320
19X-RAY DIFFRACTION19D3 - 41
20X-RAY DIFFRACTION20D42 - 119
21X-RAY DIFFRACTION21D120 - 133
22X-RAY DIFFRACTION22D134 - 191
23X-RAY DIFFRACTION23D192 - 285
24X-RAY DIFFRACTION24D286 - 320

+
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