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- PDB-4a6t: Crystal structure of the omega transaminase from Chromobacterium ... -

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Basic information

Entry
Database: PDB / ID: 4a6t
TitleCrystal structure of the omega transaminase from Chromobacterium violaceum in complex with PLP
ComponentsOMEGA TRANSAMINASE
KeywordsTRANSFERASE / PLP-BINDING ENZYME / TRANSAMINASE FOLD TYPE I
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLogan, D.T. / Hakansson, M. / Yengo, K. / Svedendahl Humble, M. / Engelmark Cassimjee, K. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P.
CitationJournal: FEBS J. / Year: 2012
Title: Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp.
Authors: Svedendahl Humble, M. / Engelmark Cassimjee, K. / Hakansson, M. / Kimbung, Y.R. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. / Logan, D.T.
History
DepositionNov 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: OMEGA TRANSAMINASE
B: OMEGA TRANSAMINASE
C: OMEGA TRANSAMINASE
D: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,1068
Polymers205,1174
Non-polymers9894
Water20,0151111
1
A: OMEGA TRANSAMINASE
B: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0534
Polymers102,5592
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint-59.2 kcal/mol
Surface area28040 Å2
MethodPISA
2
C: OMEGA TRANSAMINASE
D: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0534
Polymers102,5592
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-54.4 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.490, 62.320, 119.520
Angle α, β, γ (deg.)105.44, 90.90, 104.52
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.09338, -0.9666, -0.2386), (-0.9635, -0.1481, 0.2229), (-0.2508, 0.2091, -0.9452)-37.54, -22.66, 78.32
2given(0.9766, 0.1921, -0.09642), (-0.1948, 0.9806, -0.01924), (0.0908, 0.03757, 0.9952)6.947, 12.18, -54.2
3given(0.265, -0.8908, -0.3691), (-0.9351, -0.3309, 0.127), (-0.2353, 0.3115, -0.9207)-38.99, -44.25, -18.87

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Components

#1: Protein
OMEGA TRANSAMINASE / PROBABLE AMINOTRANSFERASE


Mass: 51279.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1111 / 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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE
Crystal growpH: 7.4
Details: DROPS OF 200 UL PROTEIN AT 12 MG/ML MIXED WITH 200 UL OF 0.1 M HEPES PH 7.5, 150-300 MM NACL AND 22.5-27.5% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04002
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: May 6, 2011 / Details: MULTILAYER MIRROR, VERTICALLY FOCUSING
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04002 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 210786 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 20.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / % possible all: 83.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6R
Resolution: 1.8→29.339 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 7186 5 %
Rwork0.1647 --
obs0.1666 143706 94.03 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.55 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7681 Å2-0.9275 Å20.9118 Å2
2--1.4724 Å20.3599 Å2
3----0.7043 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14277 0 60 1111 15448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514719
X-RAY DIFFRACTIONf_angle_d1.00819933
X-RAY DIFFRACTIONf_dihedral_angle_d13.5365315
X-RAY DIFFRACTIONf_chiral_restr0.0582069
X-RAY DIFFRACTIONf_plane_restr0.0042601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.34482110.32824013X-RAY DIFFRACTION84
1.8205-1.84190.3212380.30434530X-RAY DIFFRACTION93
1.8419-1.86440.33022390.28694535X-RAY DIFFRACTION94
1.8644-1.8880.28392410.26314573X-RAY DIFFRACTION93
1.888-1.91280.27222350.24444469X-RAY DIFFRACTION94
1.9128-1.9390.26132400.24194570X-RAY DIFFRACTION94
1.939-1.96670.27652390.234534X-RAY DIFFRACTION94
1.9667-1.9960.28252420.22594594X-RAY DIFFRACTION94
1.996-2.02720.24112390.21094536X-RAY DIFFRACTION94
2.0272-2.06050.24892400.19464575X-RAY DIFFRACTION94
2.0605-2.0960.21422390.17864534X-RAY DIFFRACTION94
2.096-2.13410.21862400.17634569X-RAY DIFFRACTION94
2.1341-2.17510.21082400.16814548X-RAY DIFFRACTION95
2.1751-2.21950.21142430.15824616X-RAY DIFFRACTION95
2.2195-2.26770.20632390.15724547X-RAY DIFFRACTION94
2.2677-2.32050.18782410.14794577X-RAY DIFFRACTION95
2.3205-2.37850.1942410.14614588X-RAY DIFFRACTION94
2.3785-2.44280.20082410.15434573X-RAY DIFFRACTION95
2.4428-2.51460.19232430.14854605X-RAY DIFFRACTION95
2.5146-2.59570.17472430.1464632X-RAY DIFFRACTION95
2.5957-2.68840.21652410.1484572X-RAY DIFFRACTION95
2.6884-2.7960.16872450.14374660X-RAY DIFFRACTION96
2.796-2.92310.19522430.14464606X-RAY DIFFRACTION95
2.9231-3.07710.19922440.14694639X-RAY DIFFRACTION96
3.0771-3.26960.1912430.15144616X-RAY DIFFRACTION96
3.2696-3.52170.19442420.15234594X-RAY DIFFRACTION95
3.5217-3.87540.17392410.14334579X-RAY DIFFRACTION94
3.8754-4.43450.15342400.12674560X-RAY DIFFRACTION94
4.4345-5.58070.16512390.14454539X-RAY DIFFRACTION94
5.5807-29.34260.19612340.17174437X-RAY DIFFRACTION92
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)
10.46550.1781-0.08711.4128-0.09412.73910.0525-0.1231-0.50950.2257-0.00560.24190.60650.0997-0.08640.3280.0127-0.07230.22830.04860.4008-24.2705-33.7949-36.301
21.2287-0.09370.80481.28250.34921.66810.1620.1291-0.3011-0.07140.0007-0.1160.31620.3201-0.1370.22740.0966-0.01980.2354-0.06060.2227-11.9948-27.6626-48.2305
31.0021-0.32940.24641.17440.04530.82230.0039-0.02610.0020.0090.0036-0.2344-0.01390.1683-0.01150.0841-0.00750.01760.16840.0230.1254-21.1342-4.0088-46.2493
40.84620.30740.25042.40480.55191.79730.07470.1236-0.1001-0.2617-0.13790.3524-0.0777-0.22210.07920.12950.0238-0.04920.24090.00560.1662-43.0031-6.5462-59.2558
51.0461-0.46990.26760.8418-0.01920.88460.060.18170.0358-0.1059-0.0165-0.1044-0.07760.1564-0.04870.12250.00280.01120.19350.01080.0999-21.7608-7.4869-54.8527
61.2689-0.1126-0.10030.89990.03091.35120.00620.4414-0.3535-0.27320.01860.23460.36180.08110.00070.31180.0724-0.1130.2473-0.13670.2778-30.2373-27.6993-64.7522
72.6234-0.8158-0.24662.48890.1711.7505-0.1055-0.1438-0.25660.1895-0.03320.09370.2544-0.22690.10420.2749-0.1085-0.05220.24230.00920.4604-44.3029-29.5487-51.9504
80.3857-0.3572-0.02110.7741-0.10811.13850.12610.1555-0.40140.12560.03180.37280.5433-0.1112-0.09370.3685-0.0059-0.13450.1857-0.09220.4721-33.9109-34.7326-55.8204
90.5119-0.15150.78651.0986-0.77241.51060.03410.35360.2408-0.29240.0047-0.2364-0.02220.3466-0.03790.2288-0.01690.07690.49480.00110.27421.5371-2.4936-45.0723
101.1970.11430.46170.95510.74731.3020.04790.1858-0.2032-0.10090.0432-0.19340.05990.2928-0.07050.13280.07050.01830.308-0.04050.1966-0.4641-17.7444-35.4977
110.9456-0.4226-0.23261.07970.24110.9772-0.0137-0.0483-0.2583-0.04810.04930.10330.2218-0.0268-0.02420.147-0.00010.00570.14040.00650.1747-23.6755-20.7658-30.6708
121.6383-0.41570.14441.07050.30652.09130.08140.43770.1729-0.1028-0.0351-0.0006-0.23810.0013-0.04010.09920.0150.01370.17890.05010.1244-25.78810.6431-29.3743
131.7670.2981-0.0340.9780.08311.20880.0360.01680.14290.0812-0.01960.0229-0.12460.0026-0.00210.13920.01490.01780.10630.01150.09-20.89173.6107-14.7601
140.4778-0.00940.06380.54430.14580.83830.01830.0482-0.08420.07940.0235-0.02890.07480.1221-0.03780.10330.0180.00990.14280.01710.1183-12.5343-11.6203-20.9896
153.4729-1.6275-1.02923.01690.79252.80580.09240.40670.3224-0.1276-0.0065-0.038-0.51510.0698-0.0840.3452-0.04460.07810.26060.06410.2267-0.517212.4922-24.4577
161.4599-0.2856-0.15472.4096-0.07331.1740.07050.13730.20070.01180.0326-0.3062-0.25220.3398-0.06390.1173-0.06430.02320.30560.01910.18066.04952.7123-23.9864
170.2333-0.14340.19461.0445-0.28252.2754-0.0855-0.2203-0.17790.32460.0780.06910.3930.15970.00650.23820.011-0.00080.13560.05040.1472-19.8381-50.54921.795
180.56710.20740.15071.02710.26740.6162-0.02370.02820.1161-0.08770.0718-0.1986-0.04710.1305-0.04350.0980.00530.03890.08220.00770.1661-8.5021-33.75388.5773
190.78840.03420.06461.22810.15520.76560.02460.00610.0543-0.176-0.06160.0759-0.1098-0.08120.02750.11140.01920.00060.05530.02390.071-35.1635-23.96917.0211
200.4585-0.09670.07990.52110.06590.44450.03280.030.1028-0.2142-0.0015-0.1027-0.1566-0.0101-0.00620.19140.00220.03130.07160.04510.1195-22.1328-24.50942.3402
211.69170.0219-0.11470.89140.1420.85580.01970.0083-0.1788-0.0158-0.06990.16510.1223-0.12550.0210.0927-0.02270.00640.0458-0.00920.0923-32.925-50.41290.9086
220.9172-0.120.48870.8056-0.4771.45340.01340.18820.2975-0.19390.0186-0.3054-0.10490.2688-0.01840.1811-0.05160.09480.1482-0.00930.3125-1.9791-15.06499.5564
230.82410.33630.08080.8950.45630.9372-0.0033-0.07010.03570.11270.1025-0.20810.13910.159-0.08210.11180.039-0.01740.11260.00470.2036-6.4067-35.707921.0495
241.5502-0.1168-0.21931.19360.36171.02780.0085-0.0250.08830.0933-0.00410.03640.0155-0.0388-0.00720.1344-0.01210.01330.11370.0110.0899-26.4961-23.93528.9567
250.82090.1699-0.00070.8982-0.10781.20090.0633-0.31840.31190.33470.0154-0.1253-0.19470.0915-0.04380.2297-0.0135-0.01550.1658-0.08560.1647-22.1123-12.335141.9579
260.6267-0.2962-0.23980.69580.40371.0415-0.0617-0.1916-0.00960.25270.1165-0.07340.16840.003-0.04690.160.0231-0.0260.11520.01220.0862-17.2046-30.60833.5714
270.3455-0.2542-0.02970.6713-0.04860.22510.0487-0.18790.24120.18160.0336-0.25440.00060.12010.03940.19220.0107-0.16330.2994-0.17960.49541.5683-15.035539.2335
282.5949-0.9065-0.81782.57040.81541.9809-0.07330.01030.20690.04570.05480.0685-0.2015-0.03090.02850.2465-0.06020.07830.1425-0.09040.5064-4.64270.146129.9382
290.8720.3303-0.1950.65740.20890.52440.0746-0.00630.23670.0260.111-0.2322-0.13330.20430.12420.1407-0.0698-0.01930.216-0.14420.49293.4373-8.155329.8855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:46)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 47:82)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 83:179)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 180:215)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 216:341)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 342:383)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 384:410)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 411:458)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 5:46)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 47:82)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 83:137)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 138:179)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 180:240)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 241:383)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 384:411)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 412:458)
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 5:46)
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 47:106)
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 107:238)
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 239:341)
21X-RAY DIFFRACTION21CHAIN C AND (RESSEQ 342:458)
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 5:46)
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 47:106)
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 107:179)
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 180:240)
26X-RAY DIFFRACTION26CHAIN D AND (RESSEQ 241:341)
27X-RAY DIFFRACTION27CHAIN D AND (RESSEQ 342:383)
28X-RAY DIFFRACTION28CHAIN D AND (RESSEQ 384:411)
29X-RAY DIFFRACTION29CHAIN D AND (RESSEQ 412:458)

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  • 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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