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- PDB-6cnz: Crystal Structure of Chorismate Mutase from Burkholderia thailandensis -

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Basic information

Entry
Database: PDB / ID: 6cnz
TitleCrystal Structure of Chorismate Mutase from Burkholderia thailandensis
ComponentsChorismate mutase
KeywordsISOMERASE / SSGCID / Chorismate mutase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Chorismate mutase, periplasmic / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Chorismate mutase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of chorismate mutase from Burkholderia thailandensis.
Authors: Asojo, O.A. / Dranow, D.M. / Serbzhinskiy, D. / Subramanian, S. / Staker, B. / Edwards, T.E. / Myler, P.J.
History
DepositionMar 9, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionMar 21, 2018ID: 4OJ7
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate mutase
B: Chorismate mutase
C: Chorismate mutase
D: Chorismate mutase
E: Chorismate mutase
F: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,77732
Polymers116,1656
Non-polymers1,61326
Water8,467470
1
A: Chorismate mutase
E: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0948
Polymers38,7222
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint1 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: Chorismate mutase
C: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,52815
Polymers38,7222
Non-polymers80613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint19 kcal/mol
Surface area14070 Å2
MethodPISA
3
D: Chorismate mutase
F: Chorismate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1569
Polymers38,7222
Non-polymers4347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-1 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.710, 121.380, 88.670
Angle α, β, γ (deg.)90.000, 99.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chorismate mutase


Mass: 19360.779 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: AQ477_14105, CRX59_12655 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B4JXW9, chorismate mutase
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: ButhA.00160.a.B2.PS01793 at 20 mg/ml was setup 1:1 with 0.8 M lithium sulfate monohydrate and 0.1 M sodium acetate Crystals were cryoprotected with 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97876 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 5, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 2.15→31.226 Å / Num. obs: 57764 / % possible obs: 98.7 % / Redundancy: 3.835 % / Biso Wilson estimate: 31.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.061 / Χ2: 0.971 / Net I/σ(I): 18.47 / Num. measured all: 221537 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.213.8890.4612.7816462429542330.8460.53598.6
2.21-2.273.8640.3543.6816073421941600.9060.41198.6
2.27-2.333.8790.2874.5115658407940370.9340.33299
2.33-2.43.8710.2355.5615145396539120.9540.27398.7
2.4-2.483.8690.1986.5414892389438490.9670.2398.8
2.48-2.573.8640.1667.8314056367836380.9760.19398.9
2.57-2.673.8510.1399.2913703360635580.980.16298.7
2.67-2.783.8390.11311.2113173347634310.9880.13198.7
2.78-2.93.8270.0913.6812591333332900.9920.10598.7
2.9-3.043.8210.06618.212030319131480.9960.07798.7
3.04-3.213.8170.05123.3611306300429620.9970.05998.6
3.21-3.43.8040.04327.5610711286128160.9980.0598.4
3.4-3.633.7890.03533.3210014268526430.9980.0498.4
3.63-3.933.7850.02939.019361249924730.9990.03499
3.93-4.33.810.02742.58767233323010.9990.03298.6
4.3-4.813.8180.02445.297858207320580.9990.02899.3
4.81-5.553.8240.02444.687033185218390.9990.02899.3
5.55-6.83.7890.02344.115930157515650.9990.02799.4
6.8-9.623.7530.01852.7645111214120210.02199
9.62-31.2263.4870.01954.8122636866490.9990.02294.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FP2
Resolution: 2.15→31.226 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.94
RfactorNum. reflection% reflection
Rfree0.216 1967 3.41 %
Rwork0.1644 --
obs0.1662 57741 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.77 Å2 / Biso mean: 43.2133 Å2 / Biso min: 15.85 Å2
Refinement stepCycle: final / Resolution: 2.15→31.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7216 0 104 470 7790
Biso mean--60.21 42.46 -
Num. residues----964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20370.27611390.21793941408098
2.2037-2.26330.24711470.19573955410299
2.2633-2.32990.25541330.1873986411999
2.3299-2.40510.24041260.17893976410299
2.4051-2.4910.25391360.18523997413399
2.491-2.59070.25881410.1824002414399
2.5907-2.70850.24891530.18623948410199
2.7085-2.85120.26881540.19193962411699
2.8512-3.02970.25841380.18873991412999
3.0297-3.26340.24551410.18083972411398
3.2634-3.59140.22461310.1723968409998
3.5914-4.11010.18371650.14053980414599
4.1101-5.17450.17491200.1324053417399
5.1745-31.22960.16041430.1414043418699
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)
15.9585-1.024-1.68020.93930.66591.3435-0.1196-0.1189-0.62970.03040.08040.01660.1598-0.07430.04620.25240.0105-0.00010.23330.01080.26795.6503-42.7379-26.4727
28.2198-0.386-0.87331.30140.42351.4022-0.3133-0.7878-0.16520.18280.24430.00480.06910.12340.06740.32130.0135-0.01480.28820.0320.23987.325-39.0409-20.4507
36.52573.67860.04115.03120.43111.7815-0.25710.46270.586-0.21160.23270.8747-0.1816-0.238-0.02640.27220.0045-0.0190.30220.06020.414-8.3775-29.0576-29.6175
45.65962.4371-2.75437.9663-0.20984.0595-0.29680.7596-0.2323-0.36270.3071-0.2326-0.0434-0.09550.06410.23390.0166-0.0460.27340.0320.15010.4469-33.702-32.7243
52.50461.3956-0.61375.1748-2.75242.29860.1689-0.00950.12450.1334-0.02150.2061-0.06250.1077-0.18170.17270.00380.01970.1888-0.00140.1795-13.0254-1.6299-45.361
63.46221.5109-1.13187.7276-4.08893.86260.0953-0.55060.00160.8726-0.17490.0025-0.56420.0480.11740.3384-0.0588-0.05990.39240.0090.3588-0.6447-5.8122-35.0154
71.7148-0.02990.41591.9733-0.98172.11020.07170.14170.0606-0.1686-0.00470.1684-0.091-0.0125-0.03870.175-0.03420.0110.16990.02120.2517-9.96791.2858-48.3531
82.2579-1.13211.16969.884-1.97243.09760.0236-0.27870.04430.74050.1751-0.3351-0.1592-0.1302-0.17690.2031-0.0173-0.00250.2721-0.01960.3073-11.0261-8.8123-36.0732
92.9085-2.9774-0.42993.24020.71672.6816-0.0469-0.050.0014-0.23520.1215-0.6630.59260.3869-0.45230.73130.382-0.27410.1435-0.17890.6452-4.2161-26.6253-44.6747
102.40710.4031-2.4556.03844.58856.7192-0.22410.329-0.42530.32690.22930.46930.6681-0.2949-0.0230.2648-0.0686-0.05020.23860.01890.3211-17.2438-19.334-50.0169
114.25833.37760.50166.5897-0.33442.30950.33520.5107-0.2243-0.7849-0.04870.60860.22650.2039-0.31870.28370.008-0.01980.2693-0.00990.2755-11.3161-11.1512-51.5487
121.4883-0.56090.1595.60292.35892.0712-0.0411-0.08820.0760.16710.1312-0.0768-0.09290.0169-0.10.2415-0.0260.04270.2161-0.00320.2267-28.062-0.652-36.4865
131.9871-1.6554-1.66145.21915.60746.28610.13780.3709-0.0315-1.1945-0.21450.3101-0.6677-0.180.11130.29710.0281-0.05890.2393-0.01130.2716-40.2358-4.7736-47.0841
141.85771.3341.20233.39562.35682.6127-0.0199-0.1715-0.11120.0380.03910.078-0.2933-0.13330.01350.27280.01650.02940.18650.00890.2652-34.192-2.0324-32.7296
154.41970.4371-5.88492.8351-0.32527.85430.4567-0.20060.26720.00280.2485-0.3432-0.40061.1758-0.59020.3098-0.0021-0.02550.2366-0.06150.4159-22.356511.056-34.7194
162.62312.15530.86917.29032.86732.9975-0.03940.16670.0804-0.3130.20370.1528-0.2453-0.0678-0.14870.1610.0202-0.01580.20490.01330.2134-30.3664-8.3106-45.907
170.39960.64281.22271.03231.95823.7248-0.2015-0.2245-1.0753-0.24181.18920.9080.7327-0.4481-0.75220.4794-0.133-0.11270.28240.13310.8036-37.4199-26.0808-37.9731
188.43240.18571.87985.02960.25057.17030.04790.1836-0.58180.46760.2594-0.15660.48910.45-0.31070.2360.0509-0.02620.1982-0.01930.2777-24.6119-18.9976-32.3271
198.7248-6.34096.49585.0798-5.25395.4365-1.1359-0.75880.39661.12810.3517-1.2506-0.96390.26350.50540.5306-0.004-0.09470.33270.00560.4689-26.4701-8.3339-28.4069
202.06932.0418-0.39653.17252.48917.15970.316-1.0657-1.29251.2846-0.36851.7220.8792-0.5250.02060.3285-0.06830.07990.27830.13480.6249-37.5317-18.2457-33.5559
218.49094.4043-1.17233.5926-1.04692.1202-0.0090.2559-0.3390.22170.2358-0.28150.0460.3254-0.24410.32710.0179-0.01630.2611-0.07010.24319.0856-35.0432-65.034
227.73884.4673-1.5012.7501-1.49232.306-0.8461.2771-1.6189-0.69360.2804-0.49790.65040.30280.46180.6008-0.00310.19990.5425-0.22680.837722.2352-44.4633-69.741
232.7967-0.3488-3.27081.68650.45324.24820.0316-0.8658-0.63340.35630.0934-0.3460.25140.6083-0.09780.4109-0.0427-0.07420.3014-0.03340.335112.3039-38.5021-59.112
244.36922.00582.73653.5946-1.74165.6514-0.28960.8393-0.17640.0646-0.13420.305-0.4522-0.63670.36920.2139-0.0318-0.02370.1934-0.01070.2215-3.0597-36.8159-67.6739
253.39733.42513.00924.15763.37854.5946-0.18131.2786-0.7511-0.04160.5993-0.5422-0.04911.1176-0.26780.3737-0.03720.02210.6728-0.14470.399121.1326-34.0944-70.5485
266.4731-2.13481.42622.0297-0.02752.1355-0.0340.19050.55720.01660.0804-0.4096-0.25340.4823-0.06090.4276-0.1190.00070.4265-0.14330.403422.8798-21.3726-59.1181
274.8167-2.3637-1.22895.55220.1544.37210.048-0.5879-0.16190.239-0.01160.0674-0.12670.05250.05340.4454-0.0936-0.09210.3671-0.08370.378315.6825-29.0215-56.9995
284.77350.15282.56551.5965-0.0062.77370.1619-0.43130.2810.0789-0.2112-0.1087-0.16060.19320.04630.3204-0.0104-0.00010.4547-0.0090.22311.8219-26.2616-12.5912
294.5347-1.86751.93174.7125-2.54363.2484-0.0976-0.5060.52950.2424-0.1783-0.0171-0.59960.25790.30670.4589-0.0501-0.03610.4512-0.12580.300112.4854-16.7819-11.6886
306.6804-2.41411.35735.5107-1.14933.21180.02960.29740.03690.0277-0.20460.051-0.04650.23080.16230.4128-0.0399-0.01210.3146-0.0920.245211.0664-23.7555-17.5863
313.56051.61860.50934.453-0.27833.53280.1075-0.83580.23360.75180.08130.1684-0.1395-0.446-0.1360.42040.03140.10330.5378-0.04420.2651-2.5297-24.3647-8.9639
323.77361.87532.56833.48922.09825.4465-0.0230.30590.3638-0.24690.16590.1642-0.8862-0.3803-0.13820.4063-0.01240.02950.54210.09540.23073.7109-24.0525-78.6924
332.72950.03131.29996.61122.46554.3963-0.2106-0.18660.721-0.1893-0.16520.0278-1.2084-0.68380.38140.71570.0806-0.10390.60480.05210.4492.5636-14.9604-78.8683
342.0157-0.41950.00022.9288-0.15812.9863-0.45160.17540.4454-0.07270.29950.0473-0.85420.09020.09320.5098-0.04340.00360.4550.06720.24224.5525-21.4606-73.0207
355.3523-1.10950.77166.0209-0.58834.7705-0.09650.80330.46-0.53710.2856-0.3293-0.60920.6931-0.20610.6222-0.16890.10050.7720.05960.375618.57-18.2573-80.1943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 118 )A35 - 118
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 154 )A119 - 154
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 175 )A155 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 195 )A176 - 195
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 69 )B33 - 69
6X-RAY DIFFRACTION6chain 'B' and (resid 70 through 90 )B70 - 90
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 132 )B91 - 132
8X-RAY DIFFRACTION8chain 'B' and (resid 133 through 154 )B133 - 154
9X-RAY DIFFRACTION9chain 'B' and (resid 155 through 159 )B155 - 159
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 175 )B160 - 175
11X-RAY DIFFRACTION11chain 'B' and (resid 176 through 194 )B176 - 194
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 69 )C35 - 69
13X-RAY DIFFRACTION13chain 'C' and (resid 70 through 90 )C70 - 90
14X-RAY DIFFRACTION14chain 'C' and (resid 91 through 118 )C91 - 118
15X-RAY DIFFRACTION15chain 'C' and (resid 119 through 132 )C119 - 132
16X-RAY DIFFRACTION16chain 'C' and (resid 133 through 154 )C133 - 154
17X-RAY DIFFRACTION17chain 'C' and (resid 155 through 159 )C155 - 159
18X-RAY DIFFRACTION18chain 'C' and (resid 160 through 175 )C160 - 175
19X-RAY DIFFRACTION19chain 'C' and (resid 176 through 189 )C176 - 189
20X-RAY DIFFRACTION20chain 'C' and (resid 190 through 197 )C190 - 197
21X-RAY DIFFRACTION21chain 'D' and (resid 35 through 69 )D35 - 69
22X-RAY DIFFRACTION22chain 'D' and (resid 70 through 90 )D70 - 90
23X-RAY DIFFRACTION23chain 'D' and (resid 91 through 118 )D91 - 118
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 132 )D119 - 132
25X-RAY DIFFRACTION25chain 'D' and (resid 133 through 156 )D133 - 156
26X-RAY DIFFRACTION26chain 'D' and (resid 157 through 175 )D157 - 175
27X-RAY DIFFRACTION27chain 'D' and (resid 176 through 194 )D176 - 194
28X-RAY DIFFRACTION28chain 'E' and (resid 34 through 69 )E34 - 69
29X-RAY DIFFRACTION29chain 'E' and (resid 70 through 118 )E70 - 118
30X-RAY DIFFRACTION30chain 'E' and (resid 119 through 156 )E119 - 156
31X-RAY DIFFRACTION31chain 'E' and (resid 157 through 193 )E157 - 193
32X-RAY DIFFRACTION32chain 'F' and (resid 36 through 69 )F36 - 69
33X-RAY DIFFRACTION33chain 'F' and (resid 70 through 118 )F70 - 118
34X-RAY DIFFRACTION34chain 'F' and (resid 119 through 156 )F119 - 156
35X-RAY DIFFRACTION35chain 'F' and (resid 157 through 193 )F157 - 193

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