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- PDB-2q1u: Crystal structure of the Bordetella bronchiseptica enzyme WbmF in... -

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Basic information

Entry
Database: PDB / ID: 2q1u
TitleCrystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and UDP
ComponentsPutative nucleotide sugar epimerase/ dehydratase
KeywordsSUGAR BINDING PROTEIN / ROSSMANN FOLD / PROTEIN-NAD+ COMPLEX / PROTEIN-UDP COMPLEX
Function / homology
Function and homology information


glutamine metabolic process / transferase activity / nucleotide binding
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / Putative nucleotide sugar epimerase/ dehydratase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHarmer, N.J. / King, J.D. / Palmer, C.M. / Maskell, D. / Blundell, T.L.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis.
Authors: King, J.D. / Harmer, N.J. / Preston, A. / Palmer, C.M. / Rejzek, M. / Field, R.A. / Blundell, T.L. / Maskell, D.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica.
Authors: Harmer, N.J. / King, J.D. / Palmer, C.M. / Preston, A. / Maskell, D.J. / Blundell, T.L.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Aug 30, 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_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_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: Putative nucleotide sugar epimerase/ dehydratase
B: Putative nucleotide sugar epimerase/ dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5098
Polymers83,1902
Non-polymers2,3196
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-46 kcal/mol
Surface area25700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.851, 79.682, 84.953
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-833-

HOH

DetailsThe biological unit is a dimer made from chains A and B.

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Components

#1: Protein Putative nucleotide sugar epimerase/ dehydratase


Mass: 41594.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BbLPS1.16, wbmF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O87989
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris, 0.2 M calcium acetate, 20 % (w/v) PEG 3000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2006
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 82675 / Num. obs: 81311 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.18 / Num. unique all: 4064 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The starting model was the related PDB entry 2PZJ, the same protein in a different crystal form. The biological unit (i.e. a dimer), generated from crystallographic symmetry, was used ...Starting model: The starting model was the related PDB entry 2PZJ, the same protein in a different crystal form. The biological unit (i.e. a dimer), generated from crystallographic symmetry, was used as the search model.
Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.969 / SU B: 2.977 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 4061 -RANDOM
Rwork0.177 ---
all0.177 82675 --
obs0.17736 81311 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.913 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å2-1.01 Å2
2--1.77 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5091 0 142 495 5728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215429
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.987434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7315697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58424.061229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38315823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.431529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024107
X-RAY DIFFRACTIONr_nbd_refined0.1990.22608
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2445
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.214
X-RAY DIFFRACTIONr_mcbond_it0.8871.53457
X-RAY DIFFRACTIONr_mcangle_it1.30225427
X-RAY DIFFRACTIONr_scbond_it2.00132248
X-RAY DIFFRACTIONr_scangle_it2.9084.51992
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.249 5244 -
Rfree-0 -
obs--85.76 %
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)
18.2377-0.10230.81724.52491.98955.84110.06350.2394-0.098-0.12630.01330.3220.0444-0.6777-0.07690.0043-0.1054-0.10040.14020.07830.0375-5.923113.81669.4282
21.0687-0.30120.92440.3133-0.99843.18290.0338-0.0776-0.16730.02640.16030.24260.2913-0.481-0.19410.0501-0.1086-0.04520.06170.05890.13-2.473910.407320.8768
320.44084.636110.0483.34756.310512.01850.05140.2209-0.2679-0.13230.12470.09210.3346-0.5929-0.17620.1155-0.1757-0.016-0.00210.0770.1135-4.40264.141627.6472
430.2599-1.05015.31747.851-5.94555.1814-0.27921.0826-0.2218-0.32540.50840.18951.3856-0.88-0.22930.1294-0.252-0.1130.12350.03910.1303-5.59242.329916.7394
52.5609-1.17770.73630.76970.14461.23520.10150.1749-0.254-0.17710.04740.14470.62610.0512-0.14890.2465-0.1021-0.0781-0.0973-0.01860.09088.56281.851713.5788
62.0455-0.05482.25420.5249-0.39524.09850.0153-0.0904-0.03150.04110.05260.09390.1968-0.1016-0.06790.0845-0.0375-0.02570.02170.02180.077711.454812.071823.812
72.7445-0.45220.96150.7931-0.58883.31820.07080.2219-0.105-0.09380.06910.09270.2425-0.0035-0.13990.0803-0.0442-0.05960.0330.01350.07129.761713.286810.5385
813.8220.16679.16570.7929-0.22166.21750.1051-0.16330.32320.16270.11410.1508-0.2260.0547-0.21920.1269-0.00030.02820.0002-0.01860.193718.271630.735721.269
91.0775-0.14350.17730.6164-0.29831.57210.08230.05690.1002-0.00790.04490.0066-0.09180.072-0.12720.061-0.0086-0.01620.04070.02280.098614.722221.100616.7627
102.2598-1.1802-0.36811.5862-0.09391.76910.0237-0.09730.01390.10060.05120.10710.185-0.0903-0.07490.0689-0.03280.0170.03090.03090.07383.840314.941437.4524
110.43170.0745-2.5749.76642.299716.11750.1644-0.5038-0.390.5473-0.0397-0.49940.51210.0329-0.12460.0635-0.04380.05860.10150.04990.067-2.474517.301849.2463
120.68150.6434-0.93112.99372.57986.28590.06410.11760.06390.15450.34430.0328-0.22390.4238-0.40840.06590.06660.076-0.00750.01080.14273.177828.421238.2753
130.8647-0.4324-0.13291.45310.09173.45570.08970.15680.1865-0.05680.11350.2598-0.3182-0.5358-0.20320.03880.0410.00310.03220.07550.1419-0.497125.978218.4221
145.41053.9182-2.13984.8266-1.18224.11520.1454-0.36930.46210.3380.08150.3167-0.4077-0.5711-0.22690.05530.03950.1080.0894-0.0070.0951-5.20827.232845.2829
1518.367221.0455-8.907224.5514-10.7296.7310.3137-0.546-0.0581.1061-0.4555-0.1195-0.4354-0.02930.14180.18840.0040.0781-0.0144-0.07510.04593.609234.665950.0367
1610.27471.7979-2.72688.2512-1.3450.8186-0.6050.9573-1.1586-0.41190.4904-0.66931.00930.22920.11470.2369-0.09120.0862-0.0015-0.11090.123911.997439.002840.0697
173.69031.9996-3.08467.16166.358513.18660.70850.04540.66210.30390.0497-0.0825-0.27880.1283-0.75830.11510.06160.0481-0.09250.06030.20433.16335.303421.1557
181.68310.3345-1.67431.8964-3.662910.05330.21920.10340.30150.1150.030.2986-0.5836-0.6039-0.2492-0.00960.07530.04110.09270.06720.139-7.563727.866727.7863
1912.8634-5.51622.68854.2404-0.90931.97740.0099-0.5521-0.61090.14930.0940.55750.3429-0.3089-0.10390.0926-0.10520.05690.02740.09370.0465-3.17037.222341.0524
2034.60426.3273-7.425935.139-3.43193.1916-0.2534-2.5563-0.48131.2059-0.1828-0.50880.3390.31810.43630.11890.0655-0.03510.20420.1314-0.103313.53185.824846.532
2111.7586-23.31562.450848.2077-8.79628.3527-0.1069-0.7660.78030.6702-0.1975-1.1976-0.00691.17570.3044-0.111-0.0023-0.11110.4256-0.05570.033553.261317.635330.8505
220.8295-0.01980.65280.4294-0.076.03210.1096-0.0517-0.0987-0.11610.0007-0.13650.40040.8167-0.1103-0.01560.0758-0.00850.17390.00690.049445.72713.158518.2986
237.681-2.06878.31928.5762-6.64611.4878-0.0299-0.20290.4159-0.28090.0185-0.7858-0.02071.08560.0114-0.09190.01630.01840.3690.00040.121255.192116.396921.2624
240.1443-0.0083-0.65620.90150.40213.13140.0775-0.0707-0.1145-0.0359-0.0852-0.22320.72730.6510.00770.07140.1730.00130.15120.02080.080445.52566.649116.3624
2513.3075-1.6092-1.74144.8747-2.828827.912-0.2105-0.0955-0.9463-0.03580.2846-0.37720.88821.3525-0.07410.0690.2441-0.00450.28920.06650.205752.99034.791422.6017
261.27140.8360.5952.47650.41193.15490.0658-0.177-0.16240.0016-0.0464-0.16450.47890.4805-0.01940.06110.098-0.03350.07390.0120.060839.30786.948925.7729
271.1927-0.27780.51850.51060.07564.05140.0130.0566-0.0729-0.0518-0.043-0.04150.27260.05450.030.09760.0114-0.02420.0228-0.01370.074828.836911.61915.0946
282.241-0.15940.49990.46340.0531.5380.1179-0.07660.1973-0.0869-0.0104-0.0459-0.03810.2999-0.10750.0344-0.0287-0.03340.0493-0.01140.061232.4421.539323.9628
291.1108-0.1595-0.05460.5908-0.053.20520.0816-0.07870.12430.00160.015-0.0035-0.13060.1225-0.09660.0445-0.0207-0.01710.0556-0.02750.084629.978221.162323.5743
302.86981.97190.06254.40940.77743.61910.08350.0454-0.04170.0475-0.0218-0.19390.17650.4853-0.0616-0.00170.0410.03360.12150.01620.003643.194316.16065.5907
313.19192.6136-2.2332.1858-2.08482.9984-0.08120.17430.0353-0.32860.0113-0.02770.35850.1320.06990.10350.06040.04430.1056-0.01340.02139.536414.6537-1.8733
324.1887-1.8021-0.63193.24410.24734.25950.22060.2953-0.0714-0.3251-0.26060.2665-0.03360.09670.040.06680.00160.07710.05120.05380.004841.709625.3632-6.8979
330.5312-0.3083-0.68550.8451-0.16613.6610.1958-0.13740.2604-0.0621-0.1113-0.2041-0.38460.6396-0.0845-0.0146-0.10130.04850.1205-0.0040.08745.946427.441310.6166
344.2992.31784.00584.5022-3.610913.9703-0.59191.67370.6217-0.3578-0.2409-0.4392-0.19530.33320.83270.20320.04240.07250.18640.07-0.037346.040926.4804-14.9118
3514.6966-12.0332-11.100218.56411.711918.07670.25990.080.4351-0.38270.0378-0.3559-0.35590.4307-0.29770.1494-0.01130.0051-0.0620.0859-0.023436.977139.4355-8.9666
367.41424.13334.52212.52372.58832.77870.1261-0.9577-0.63770.20090.51140.48950.8564-1.2053-0.63750.23440.05550.10640.06720.10090.072732.246538.7823-0.4645
371.2284-0.1857-0.12151.46241.05593.47230.1896-0.20150.4414-0.10990.0534-0.2726-0.60790.8249-0.2430.0375-0.17890.05130.2032-0.00790.141648.380232.174714.6484
386.61013.914-0.255210.86643.11924.17890.05110.1308-0.23960.0688-0.1206-0.62350.44241.06880.0695-0.02070.12750.09610.25310.0410.013353.726913.7761-0.0024
3918.21721.0975-2.29731.98521.27642.2504-0.21660.5607-0.8062-0.28530.0451-0.41080.74330.36070.17150.20710.1360.10420.0549-0.0433-0.017242.87964.4602-3.2939
4030.9436-17.3822-4.361729.13163.94736.1806-0.77131.8461-0.8236-1.34280.08960.35560.49650.04330.68170.211-0.0299-0.02950.219-0.1032-0.144531.23645.7438-7.3663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 1628 - 36
2X-RAY DIFFRACTION2AA17 - 4937 - 69
3X-RAY DIFFRACTION3AA50 - 5670 - 76
4X-RAY DIFFRACTION4AA57 - 6277 - 82
5X-RAY DIFFRACTION5AA63 - 7883 - 98
6X-RAY DIFFRACTION6AA79 - 10699 - 126
7X-RAY DIFFRACTION7AA107 - 131127 - 151
8X-RAY DIFFRACTION8AA132 - 155152 - 175
9X-RAY DIFFRACTION9AA156 - 188176 - 208
10X-RAY DIFFRACTION10AA189 - 219209 - 239
11X-RAY DIFFRACTION11AA220 - 229240 - 249
12X-RAY DIFFRACTION12AA230 - 243250 - 263
13X-RAY DIFFRACTION13AA244 - 270264 - 290
14X-RAY DIFFRACTION14AA271 - 287291 - 307
15X-RAY DIFFRACTION15AA288 - 297308 - 317
16X-RAY DIFFRACTION16AA298 - 303318 - 323
17X-RAY DIFFRACTION17AA304 - 311324 - 331
18X-RAY DIFFRACTION18AA312 - 332332 - 352
19X-RAY DIFFRACTION19AA333 - 349353 - 369
20X-RAY DIFFRACTION20AA350 - 355370 - 375
21X-RAY DIFFRACTION21BB8 - 1328 - 33
22X-RAY DIFFRACTION22BB14 - 2934 - 49
23X-RAY DIFFRACTION23BB30 - 3650 - 56
24X-RAY DIFFRACTION24BB37 - 5557 - 75
25X-RAY DIFFRACTION25BB56 - 6176 - 81
26X-RAY DIFFRACTION26BB62 - 8682 - 106
27X-RAY DIFFRACTION27BB87 - 116107 - 136
28X-RAY DIFFRACTION28BB117 - 158137 - 178
29X-RAY DIFFRACTION29BB159 - 188179 - 208
30X-RAY DIFFRACTION30BB189 - 202209 - 222
31X-RAY DIFFRACTION31BB203 - 221223 - 241
32X-RAY DIFFRACTION32BB222 - 239242 - 259
33X-RAY DIFFRACTION33BB240 - 285260 - 305
34X-RAY DIFFRACTION34BB286 - 291306 - 311
35X-RAY DIFFRACTION35BB292 - 297312 - 317
36X-RAY DIFFRACTION36BB298 - 305318 - 325
37X-RAY DIFFRACTION37BB306 - 328326 - 348
38X-RAY DIFFRACTION38BB329 - 341349 - 361
39X-RAY DIFFRACTION39BB342 - 349362 - 369
40X-RAY DIFFRACTION40BB350 - 355370 - 375

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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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