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- PDB-4gug: 1.62 Angstrom Crystal Structure of the Salmonella enterica 3-Dehy... -

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Basic information

Entry
Database: PDB / ID: 4gug
Title1.62 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) E86A Mutant in Complex with Dehydroshikimate (Crystal Form #1)
Components3-dehydroquinate dehydratase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / TIM barrel
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3DS / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLight, S.H. / Minasov, G. / Duban, M.-E. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Protein Sci. / Year: 2013
Title: Reassessing the type I dehydroquinate dehydratase catalytic triad: Kinetic and structural studies of Glu86 mutants.
Authors: Light, S.H. / Anderson, W.F. / Lavie, A.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4665
Polymers60,0872
Non-polymers3803
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-28 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.703, 64.266, 81.045
Angle α, β, γ (deg.)90.00, 93.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase


Mass: 30043.273 Da / Num. of mol.: 2 / Mutation: E86A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: aroD, STM1358 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P58687, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-3DS / (4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid / 3-dehydroshikimate


Mass: 172.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 3 mM dehydroquinic acid, crystallization condition: 0.19 M sodium chloride, 17.9% w/v PEG3350, VAPOR DIFFUSION, SITTING ...Details: protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 3 mM dehydroquinic acid, crystallization condition: 0.19 M sodium chloride, 17.9% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2012 / Details: Bimorph K-B pair
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.62→30 Å / Num. all: 57849 / Num. obs: 57849 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.2
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2802 / % possible all: 95

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L2I
Resolution: 1.62→29.86 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.389 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20827 2908 5 %RANDOM
Rwork0.17349 ---
all0.17531 54916 --
obs0.17531 54916 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.376 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-0 Å22.09 Å2
2--1.17 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.62→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 24 359 4133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194018
X-RAY DIFFRACTIONr_bond_other_d0.0010.024001
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.975477
X-RAY DIFFRACTIONr_angle_other_deg0.86239216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2165536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66824.242165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98315731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1491528
X-RAY DIFFRACTIONr_chiral_restr0.120.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024549
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 214 -
Rwork0.3 3864 -
obs--93.47 %
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)
123.4976-0.2997-0.58745.2743-0.11564.3007-0.09030.22650.6011-0.09140.06830.2427-0.15420.06550.0220.2083-0.0138-0.05520.00510.00430.22619.77884.019931.1365
26.8477-4.65275.07868.2535-5.91427.2741-0.20910.2983-0.17450.06520.17630.0934-0.18710.21760.03270.1469-0.0344-0.02110.0645-0.01380.217425.6004-6.975628.9422
34.48333.1386-3.67926.2747-8.332311.15920.07590.158-0.3486-0.0969-0.1425-0.07590.20770.26670.06660.3320.10760.01010.21170.01710.428439.3333-13.37137.9123
414.4336-4.06175.87916.6449-7.70249.0513-0.33540.8591-0.06970.273-0.1271-0.416-0.32030.28160.46260.3375-0.0348-0.00810.3846-0.01490.387236.1763-5.763326.8239
52.86210.79811.31412.6197-1.78795.8177-0.03590.0605-0.2880.1502-0.0309-0.21310.04750.17860.06680.11820.017-0.03050.0093-0.00530.256329.253-11.798339.0168
64.76222.7881-1.02944.2778-3.05622.56550.2058-0.5425-0.37650.2249-0.2762-0.3128-0.08150.16190.07040.24330.0187-0.08870.22940.01950.341635.2306-9.538348.5029
716.0473-9.93314.444613.4028-2.55546.0282-0.31370.08540.25740.31330.0755-0.1073-0.44450.30920.23810.1211-0.0513-0.05750.08690.04150.29437.4107-1.383236.2844
83.42682.0328-0.18273.3519-0.81573.23910.0417-0.0024-0.26490.124-0.0228-0.11150.0161-0.1105-0.01890.1246-0.0028-0.03810.00560.01350.258724.404-10.678240.2404
92.09771.7867-0.1124.0371-0.53832.11510.1004-0.244-0.11290.2832-0.1199-0.22220.0252-0.00940.01950.164-0.0116-0.06910.03210.01960.237324.062-9.076948.4548
101.38961.2330.1932.76960.3812.1630.1105-0.2570.11170.3332-0.22270.07710.048-0.36370.11230.1532-0.0373-0.02410.1014-0.02810.212213.8975-5.708447.6542
112.99735.15052.27989.18974.87824.5510.055-0.00720.1180.0457-0.05640.1222-0.1392-0.15780.00140.16850.0161-0.06070.0175-0.01150.265119.3464-0.379343.1246
121.6205-0.25740.40951.37431.12872.0902-0.0201-0.1844-0.09870.1476-0.11770.15670.1847-0.27430.13770.1193-0.0281-0.01260.0529-0.0170.23596.6807-14.001635.3195
131.56250.35420.76951.88941.28842.3204-0.0272-0.0751-0.03590.0021-0.05820.10550.0747-0.16090.08540.1304-0.01-0.02690.01270.00490.22310.5062-14.29830.4957
143.1404-1.0559-0.97954.46482.0553.7064-0.03240.05530.2104-0.2330.0140.1469-0.2071-0.34230.01840.13440.0197-0.0580.048-0.00510.26844.9443-7.400325.8381
153.40650.7421.68961.6420.14172.3959-0.22-0.23880.31110.07570.08890.1339-0.1886-0.190.13110.17140.0148-0.04530.0717-0.00920.273210.674-3.835631.6429
162.25982.24540.17488.1627-2.60663.8651-0.21360.32-0.0741-0.44720.1184-0.12150.2830.29780.09520.1632-0.0103-0.01570.06490.00460.240617.1983-17.110822.0063
177.57870.20511.10070.20310.89454.20020.01970.50550.3149-0.1323-0.05370.026-0.5301-0.04340.0340.24610.0209-0.06580.14810.01930.314513.5488-5.192121.9437
1823.7781-9.5241-3.76118.60764.67922.707-0.05880.1458-0.38570.30440.1528-0.04770.17130.1598-0.0940.1866-0.0301-0.02540.2064-0.020.215627.9882-13.792226.2401
191.9836-1.82090.98734.2607-2.80417.2021-0.04450.3087-0.0913-0.14780.20090.0174-0.0370.4355-0.15640.1166-0.0659-0.02570.2176-0.01980.202926.3104-11.469520.1024
2015.7692-3.063-5.66659.60732.72289.69170.27070.36480.1512-0.7436-0.25370.0819-0.6107-0.0404-0.0170.2606-0.0975-0.04330.09740.06690.131521.4167-3.402513.1568
2116.4140.92094.68372.84421.14471.62370.53671.1014-2.52030.05660.1525-0.09660.23560.3822-0.68920.8850.22250.19520.3459-0.18560.502817.3202-27.7968-4.7627
228.56876.11051.05154.67532.25577.54960.00680.1701-0.46210.16680.1028-0.30770.62080.3686-0.10960.2911-0.0760.02470.3911-0.12340.273517.9929-22.85023.1975
230.6069-1.56131.17894.2214-4.2249.59120.0669-0.02640.0499-0.1062-0.0483-0.0882-0.14480.3576-0.01860.2555-0.1811-0.04050.2844-0.04180.196518.1141-7.0508-13.8657
241.4836-0.9740.10141.8849-2.64986.53590.03350.18750.12440.0442-0.0586-0.0024-0.23880.32910.02510.2833-0.1271-0.03460.3017-0.01470.223515.2395-11.2007-11.1712
2512.0448-4.7682-1.7166.67070.01752.7826-0.3431-0.2367-0.785-0.3750.22610.33610.0332-0.48280.1170.2248-0.1577-0.01660.30060.02870.106810.6223-12.5131-23.784
2613.79022.5737-5.565715.62219.254110.602-0.3671-0.9192-0.2864-0.10550.2771-0.49670.32690.02830.090.2324-0.10660.03060.4755-0.02990.171221.9273-16.8677-16.0281
276.5631-0.00971.20450.32630.8252.3668-0.07020.19180.1587-0.05140.01620.0204-0.0761-0.04010.0540.2698-0.1111-0.04010.26690.00530.19979.9155-14.9391-9.9219
284.346-4.4114-3.92376.09072.55376.2756-0.2010.6112-0.1602-0.35690.06040.26240.4138-0.9990.14060.3323-0.2941-0.10090.5088-0.03040.14261.932-17.2223-18.3035
2914.2483-6.1353-5.02494.97844.11836.9743-0.14570.0247-0.2647-0.31070.0640.15910.4709-0.46320.08180.2375-0.1708-0.04210.22950.00940.09773.6277-19.6834-8.587
3016.71094.1889-0.1142.07750.73870.5763-0.8250.4701-0.6963-0.18990.24950.57960.02440.04790.57540.5546-0.266-0.06870.9107-0.01010.635-6.4829-23.7899-10.4842
3112.97421.7922-2.49397.0996-2.281810.5332-0.43180.9563-0.8036-0.68270.3662-0.13240.5674-0.26130.06560.3924-0.30490.03020.3516-0.1680.20644.8387-28.6747-14.4902
322.3999-4.4309-2.775812.11047.77987.6297-0.04420.38870.2991-0.328-0.0191-0.2877-0.0733-0.73540.06330.1702-0.1192-0.08240.40530.03110.16790.9324-13.9549-1.2818
333.2831.7485-0.05867.7695-0.66593.5833-0.24390.32080.24890.13490.14740.48540.3482-0.84440.09650.1156-0.1464-0.04850.26020.01110.1931-4.0757-18.75497.8544
3416.352-9.1193-4.52796.85.466.33620.1523-0.1334-0.28510.1322-0.20270.12750.4822-0.52180.05040.4354-0.26050.01260.3054-0.03710.2756-1.8459-26.2916-1.829
351.03280.07010.33082.11240.76154.0598-0.19840.21050.1404-0.04090.13940.17140.1058-0.45930.0590.1354-0.0439-0.06040.15390.02640.22573.3064-14.101210.2837
3621.76177.08919.12615.9184-0.483619.73250.0453-0.38120.14320.28250.1343-0.08370.7104-0.5985-0.17970.2638-0.0750.00550.1065-0.05690.17912.0522-27.806712.3149
371.6942-0.0086-0.64874.27980.1253.7608-0.20240.1770.1424-0.09930.08850.22570.1147-0.11630.11390.1481-0.0713-0.03950.1617-0.00260.13919.2943-15.00256.9924
381.81631.1883-0.89780.903-1.25867.1361-0.03560.2773-0.0133-0.03390.08050.0740.2778-0.0169-0.04490.2172-0.058-0.02850.2291-0.04090.214814.4466-16.86865.9594
390.85350.3960.30751.5002-0.07114.4077-0.10920.17030.0901-0.13740.12260.0531-0.26730.3554-0.01330.2163-0.137-0.02750.23620.00780.161818.9149-8.58212.4931
409.71664.7819-2.3498.6119-4.73324.13980.04810.1935-0.45450.17420.0483-0.42290.12930.3314-0.09650.2370.021-0.04160.2143-0.05580.231224.1537-19.018612.9225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 12
2X-RAY DIFFRACTION2A13 - 24
3X-RAY DIFFRACTION3A25 - 37
4X-RAY DIFFRACTION4A38 - 42
5X-RAY DIFFRACTION5A43 - 53
6X-RAY DIFFRACTION6A54 - 68
7X-RAY DIFFRACTION7A69 - 74
8X-RAY DIFFRACTION8A75 - 85
9X-RAY DIFFRACTION9A86 - 113
10X-RAY DIFFRACTION10A114 - 132
11X-RAY DIFFRACTION11A133 - 141
12X-RAY DIFFRACTION12A142 - 162
13X-RAY DIFFRACTION13A163 - 183
14X-RAY DIFFRACTION14A184 - 194
15X-RAY DIFFRACTION15A195 - 203
16X-RAY DIFFRACTION16A204 - 215
17X-RAY DIFFRACTION17A216 - 223
18X-RAY DIFFRACTION18A224 - 229
19X-RAY DIFFRACTION19A235 - 246
20X-RAY DIFFRACTION20A247 - 251
21X-RAY DIFFRACTION21B3 - 10
22X-RAY DIFFRACTION22B11 - 18
23X-RAY DIFFRACTION23B19 - 37
24X-RAY DIFFRACTION24B38 - 55
25X-RAY DIFFRACTION25B56 - 67
26X-RAY DIFFRACTION26B68 - 74
27X-RAY DIFFRACTION27B75 - 84
28X-RAY DIFFRACTION28B91 - 109
29X-RAY DIFFRACTION29B110 - 118
30X-RAY DIFFRACTION30B119 - 126
31X-RAY DIFFRACTION31B127 - 136
32X-RAY DIFFRACTION32B137 - 147
33X-RAY DIFFRACTION33B148 - 159
34X-RAY DIFFRACTION34B160 - 167
35X-RAY DIFFRACTION35B168 - 191
36X-RAY DIFFRACTION36B192 - 195
37X-RAY DIFFRACTION37B196 - 215
38X-RAY DIFFRACTION38B216 - 228
39X-RAY DIFFRACTION39B229 - 246
40X-RAY DIFFRACTION40B247 - 251

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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

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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

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