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- PDB-38le: Crystal Structure of L-erythrulose-1-phosphate isomerase from Bru... -

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Basic information

Entry
Database: PDB / ID: 38le
TitleCrystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with ETHYL DIHYDROGEN PHOSPHATE
ComponentsL-erythrulose-1-phosphate isomerase
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / L-erythrulose-1-phosphate isomerase / Brucella melitensis
Function / homology
Function and homology information


L-erythrulose-1-phosphate isomerase / triose-phosphate isomerase activity / glycerol catabolic process / glyceraldehyde-3-phosphate biosynthetic process / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
ETHYL DIHYDROGEN PHOSPHATE / HEXANE-1,6-DIOL / L-erythrulose-1-phosphate isomerase
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of L-erythrulose-1-phosphate isomerase from Brucella melitensis in complex with ETHYL DIHYDROGEN PHOSPHATE
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionSep 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-erythrulose-1-phosphate isomerase
B: L-erythrulose-1-phosphate isomerase
C: L-erythrulose-1-phosphate isomerase
D: L-erythrulose-1-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,96220
Polymers114,9794
Non-polymers98316
Water18,2671014
1
A: L-erythrulose-1-phosphate isomerase
D: L-erythrulose-1-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,02711
Polymers57,4892
Non-polymers5389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-69 kcal/mol
Surface area17650 Å2
MethodPISA
2
B: L-erythrulose-1-phosphate isomerase
C: L-erythrulose-1-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9359
Polymers57,4892
Non-polymers4457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-55 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.318, 49.513, 116.429
Angle α, β, γ (deg.)88.44, 83.14, 86.18
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-erythrulose-1-phosphate isomerase / D-3-tetrulose-4-phosphate isomerase


Mass: 28744.627 Da / Num. of mol.: 4 / Fragment: K3-N256 / Mutation: A173D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: eryH, tpiA-2, BAB2_0367 / Plasmid: BrabA.00276.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2YIQ6, L-erythrulose-1-phosphate isomerase

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Non-polymers , 6 types, 1030 molecules

#2: Chemical ChemComp-EFS / ETHYL DIHYDROGEN PHOSPHATE


Mass: 126.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7O4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1014 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), EFS fit best to the electron ...Details: 70 mM MES pH 6.5, 70 mM CaCl2, 14% PEG 1500, 8.4% hexanediol. BrabA.00276.a.B2.PW39519 at 15.2 mg/mL. 20 hour soak in 10 mM glycerol 3-phosphate (D/L mixture), EFS fit best to the electron density, plate Liu-S-202 E9-F10, Puck: PSL-0208, Cryo: 100 mM MES, pH 6.5, 100 mM CaCl2, 20% PEG 1500, 12% hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 22, 2026
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.5→45.74 Å / Num. obs: 152470 / % possible obs: 95 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.048 / Rrim(I) all: 0.09 / Χ2: 0.96 / Net I/σ(I): 10.1 / Num. measured all: 546898
Reflection shellResolution: 1.5→1.54 Å / % possible obs: 87.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.642 / Num. measured all: 34260 / Num. unique obs: 10484 / CC1/2: 0.707 / Rpim(I) all: 0.414 / Rrim(I) all: 0.767 / Χ2: 0.78 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.2_6151: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.74 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 7874 5.17 %
Rwork0.1519 --
obs0.1533 152427 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7549 0 55 1014 8618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077816
X-RAY DIFFRACTIONf_angle_d0.87710593
X-RAY DIFFRACTIONf_dihedral_angle_d17.9952863
X-RAY DIFFRACTIONf_chiral_restr0.0521187
X-RAY DIFFRACTIONf_plane_restr0.0121376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28672610.27884389X-RAY DIFFRACTION87
1.52-1.530.25942140.2524525X-RAY DIFFRACTION88
1.53-1.550.23552480.23434601X-RAY DIFFRACTION90
1.55-1.570.23372570.21574699X-RAY DIFFRACTION93
1.57-1.590.24032620.20434814X-RAY DIFFRACTION95
1.59-1.620.2062800.19794816X-RAY DIFFRACTION95
1.62-1.640.23082550.19184774X-RAY DIFFRACTION95
1.64-1.660.21572720.1814919X-RAY DIFFRACTION95
1.66-1.690.21052820.18014760X-RAY DIFFRACTION95
1.69-1.720.21712790.17114818X-RAY DIFFRACTION96
1.72-1.750.1882530.16514879X-RAY DIFFRACTION96
1.75-1.780.20332500.16624824X-RAY DIFFRACTION96
1.78-1.810.19462700.16764909X-RAY DIFFRACTION96
1.81-1.850.1832880.16564837X-RAY DIFFRACTION96
1.85-1.890.20352780.1694894X-RAY DIFFRACTION96
1.89-1.930.17722790.15584809X-RAY DIFFRACTION96
1.93-1.980.17312710.14934890X-RAY DIFFRACTION96
1.98-2.040.18052790.15034866X-RAY DIFFRACTION96
2.04-2.10.17552570.14444875X-RAY DIFFRACTION96
2.1-2.160.20182590.14874988X-RAY DIFFRACTION97
2.16-2.240.17512660.13984853X-RAY DIFFRACTION96
2.24-2.330.16732510.13664847X-RAY DIFFRACTION96
2.33-2.440.1692670.13334866X-RAY DIFFRACTION96
2.44-2.560.15962560.13794923X-RAY DIFFRACTION96
2.56-2.730.1722620.1424905X-RAY DIFFRACTION96
2.73-2.940.18392750.14544855X-RAY DIFFRACTION96
2.94-3.230.16552220.14234886X-RAY DIFFRACTION95
3.23-3.70.17062730.13664798X-RAY DIFFRACTION95
3.7-4.660.14652480.12634818X-RAY DIFFRACTION95
4.66-45.740.19232600.16114916X-RAY DIFFRACTION97
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)
10.70110.29070.5454.49342.60853.78470.05550.0119-0.0258-0.1836-0.08250.09410.0391-0.07180.04190.11770.0027-0.00310.11650.02480.11261.18456.4612-4.0528
23.61792.65764.30694.19064.27216.0826-0.17560.09190.1622-0.4491-0.03920.2458-0.4053-0.0730.23380.18920.0058-0.0320.12280.02860.1205-4.266416.4178-9.2473
30.7041-0.19930.16691.08070.12863.18670.0336-0.0029-0.0545-0.0628-0.06040.09940.0933-0.16190.03240.0993-0.0139-0.01280.10060.00690.1251-6.45216.74813.4276
40.94750.52750.60671.85430.1291.87680.0842-0.0216-0.14440.0637-0.0117-0.2990.10210.2034-0.0210.14440.0104-0.0190.12170.02670.18113.7614-4.70218.5666
54.90820.5402-2.27753.60641.13393.17520.035-0.2128-0.3509-0.00530.0865-0.33860.17770.2053-0.11760.14120.0056-0.03320.08280.0470.1599-0.1343-14.12068.2876
65.73261.0705-2.80133.4512-0.49484.6994-0.0807-0.1315-0.0535-0.1331-0.0091-0.3783-0.10090.41060.07040.1666-0.0095-0.03920.08830.03610.15351.8735-7.63780.2563
71.8392.417-1.58335.1209-2.73482.2215-0.07530.063-0.1914-0.306-0.0532-0.28860.10910.05650.13750.17830.0075-0.00010.1343-0.01450.15753.86-11.4397-4.6699
81.92771.7541-0.03222.26481.02093.3719-0.10510.0811-0.0845-0.220.1099-0.11560.13190.0805-0.05530.17570.02210.01860.12750.01870.13056.0088-1.3365-10.2874
97.0292-0.6492-0.6156.64644.15657.27580.04130.5339-0.1804-0.669-0.0504-0.00680.10140.0034-0.0440.26630.00650.00490.16710.00640.0972.15923.7405-17.4466
101.81532.41041.71686.65834.36725.6750.01020.0380.04720.1580.02430.02580.1581-0.0118-0.03030.08040.00680.0140.12160.01250.1222-1.17175.0036-45.3564
116.25216.00561.06499.07763.5043.91840.3021-0.3107-0.00380.7905-0.32210.21940.2093-0.16880.01640.2008-0.04330.03350.17880.00710.1494-3.92212.1697-33.3879
121.8137-0.1132-0.0160.5325-0.40132.961-0.02160.0781-0.1234-0.01250.03770.08930.2829-0.1746-0.00890.0999-0.01340.00860.08350.00310.1045-1.8034-2.3234-43.6879
135.14993.4929-0.95664.0259-2.16832.05420.0715-0.0785-0.19720.122-0.0508-0.09160.0711-0.0359-0.02970.1130.01020.00090.0799-0.00590.09166.09670.44-39.4804
140.7910.16230.53721.2842-0.051.58970.01290.0759-0.00150.0221-0.0035-0.1-0.04980.0753-0.00530.0957-0.00230.00230.12910.00750.138115.03378.2003-48.3681
152.519-3.04973.91774.5888-4.86496.7469-0.1912-0.0170.08470.122-0.0153-0.1018-0.2599-0.02190.23830.1133-0.005-0.00390.1539-0.01030.14534.863612.2808-60.9082
167.3963-4.11853.61416.8575-2.68095.7739-0.1350.31790.126-0.3668-0.0249-0.17770.05210.18270.15710.0973-0.0060.04010.16650.00160.077513.42655.689-64.4728
176.4611-2.60921.75684.9789-1.06194.1827-0.06110.11740.2603-0.0285-0.02360.1375-0.2396-0.22020.02470.1124-0.02680.00110.1275-0.01070.09633.89944.9317-59.0852
183.3478-0.7801-1.70831.66310.96254.5940.02360.0987-0.159-0.1321-0.0290.1647-0.0017-0.1250.00270.109-0.0073-0.02770.1029-0.01450.1198-0.25772.9843-63.1571
191.7118-0.3465-0.82591.66641.89434.0152-0.03240.1649-0.02-0.069-0.13660.2395-0.0596-0.42180.17230.10140.0058-0.00090.16640.00010.1438-7.56843.4726-54.7691
205.95812.21993.34735.99631.18537.6362-0.15860.1331-0.0176-0.0802-0.03610.3810.0527-0.68690.17940.0828-0.02320.03170.2131-0.01120.1923-12.6596-0.8782-48.3303
212.1861-0.26290.56630.6006-0.58460.6314-0.0505-0.220.22710.3046-0.0154-0.0448-0.0681-0.05670.07210.1908-0.0388-0.0230.13350.00970.153321.726620.1864-28.2088
222.07561.45143.16843.67264.32747.05340.1836-0.2677-0.11110.4676-0.1851-0.16620.6916-0.22740.03130.2421-0.0258-0.05770.14460.04240.160822.28575.5507-23.9287
231.92050.06081.11370.9643-0.09791.89030.0103-0.19030.08960.2131-0.0711-0.006-0.0626-0.08630.06220.162-0.0173-0.00740.1048-0.0040.109314.128317.2132-29.3185
242.8965-1.9713-2.86372.61521.84074.33670.05980.12390.0157-0.0929-0.09660.0114-0.175-0.10060.02790.1363-0.0236-0.03290.08970.0150.126714.259126.1433-42.1183
253.7071.7799-2.62552.3437-1.24584.03440.01230.0962-0.2877-0.0788-0.0561-0.3402-0.10590.26990.04670.18530.0062-0.00750.1471-0.01790.186823.385530.3843-40.8891
264.22922.7844-3.96812.4541-2.44814.69180.06240.2932-0.0534-0.01160.0824-0.1317-0.10980.0051-0.0540.1926-0.0274-0.01610.11920.0080.197521.734637.4644-42.0433
278.628-2.3529-0.82762.1575-0.45262.05750.08180.0844-0.04940.1028-0.0667-0.0927-0.03570.0499-0.01280.2054-0.0484-0.04830.0559-0.0010.134417.875733.4532-33.2517
281.9654-1.1724-0.113.2946-0.00760.56370.09560.0611-0.00120.1516-0.1436-0.2188-0.13430.09420.04640.216-0.0498-0.06320.14040.02690.190928.109433.9818-32.0985
291.60181.85210.27083.44280.97840.8203-0.04990.06010.10950.169-0.0533-0.498-0.15780.11170.04370.2028-0.04-0.08670.1430.0380.23332.774423.5302-29.1835
306.22964.88882.30224.7553.72654.9422-0.0568-0.18320.19880.5309-0.034-0.5094-0.18190.2604-0.03490.2756-0.0133-0.15150.17040.02290.254134.532218.5096-21.1472
311.875-0.59550.31091.71620.08451.9131-0.039-0.09450.21190.11890.01960.0332-0.171-0.00460.00840.1028-0.00720.01350.12050.00370.1175-6.582624.715322.0527
320.24320.06650.14730.34910.01040.66190.0163-0.0465-0.00410.048-0.0064-0.03010.04210.0527-0.0140.1073-0.0003-0.00090.13850.01450.12277.03416.071919.8758
332.30890.13620.12130.6725-0.10881.57060.0501-0.28510.01080.1517-0.02220.0166-0.0275-0.064-0.03210.1614-0.0019-0.00520.1425-0.00210.11523.050921.456433.4911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 139 )
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 158 )
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 217 )
8X-RAY DIFFRACTION8chain 'A' and (resid 218 through 238 )
9X-RAY DIFFRACTION9chain 'A' and (resid 239 through 254 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 15 )
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 28 )
12X-RAY DIFFRACTION12chain 'B' and (resid 29 through 47 )
13X-RAY DIFFRACTION13chain 'B' and (resid 48 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 119 )
15X-RAY DIFFRACTION15chain 'B' and (resid 120 through 139 )
16X-RAY DIFFRACTION16chain 'B' and (resid 140 through 158 )
17X-RAY DIFFRACTION17chain 'B' and (resid 159 through 182 )
18X-RAY DIFFRACTION18chain 'B' and (resid 183 through 217 )
19X-RAY DIFFRACTION19chain 'B' and (resid 218 through 238 )
20X-RAY DIFFRACTION20chain 'B' and (resid 239 through 253 )
21X-RAY DIFFRACTION21chain 'C' and (resid -3 through 15 )
22X-RAY DIFFRACTION22chain 'C' and (resid 16 through 28 )
23X-RAY DIFFRACTION23chain 'C' and (resid 29 through 96 )
24X-RAY DIFFRACTION24chain 'C' and (resid 97 through 119 )
25X-RAY DIFFRACTION25chain 'C' and (resid 120 through 139 )
26X-RAY DIFFRACTION26chain 'C' and (resid 140 through 151 )
27X-RAY DIFFRACTION27chain 'C' and (resid 152 through 182 )
28X-RAY DIFFRACTION28chain 'C' and (resid 183 through 217 )
29X-RAY DIFFRACTION29chain 'C' and (resid 218 through 238 )
30X-RAY DIFFRACTION30chain 'C' and (resid 239 through 254 )
31X-RAY DIFFRACTION31chain 'D' and (resid -3 through 47 )
32X-RAY DIFFRACTION32chain 'D' and (resid 48 through 151 )
33X-RAY DIFFRACTION33chain 'D' and (resid 152 through 254 )

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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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