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- PDB-2bwp: 5-Aminolevulinate Synthase from Rhodobacter capsulatus in complex... -

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Basic information

Entry
Database: PDB / ID: 2bwp
Title5-Aminolevulinate Synthase from Rhodobacter capsulatus in complex with glycine
Components5-AMINOLEVULINATE SYNTHASE
KeywordsTRANSFERASE / TETRAPYRROLE BIOSYNTHESIS / HEME BIOSYNTHESIS / PYRIDOXAL PHOSPHATE DEPENDENT / ACYLTRANSFERASE
Function / homology
Function and homology information


5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / protoporphyrinogen IX biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
ACETIC ACID / Chem-PLG / 5-aminolevulinate synthase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsAstner, I. / Schulze, J.O. / Van Den Heuvel, J.J. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.
CitationJournal: Embo J. / Year: 2005
Title: Crystal Structure of 5-Aminolevulinate Synthase, the First Enzyme of Heme Biosynthesis, and its Link to Xlsa in Humans.
Authors: Astner, I. / Schulze, J.O. / Van Den Heuvel, J.J. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.
History
DepositionJul 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-AMINOLEVULINATE SYNTHASE
B: 5-AMINOLEVULINATE SYNTHASE
D: 5-AMINOLEVULINATE SYNTHASE
E: 5-AMINOLEVULINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,10111
Polymers174,6964
Non-polymers1,4057
Water2,126118
1
A: 5-AMINOLEVULINATE SYNTHASE
B: 5-AMINOLEVULINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0205
Polymers87,3482
Non-polymers6723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: 5-AMINOLEVULINATE SYNTHASE
E: 5-AMINOLEVULINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0806
Polymers87,3482
Non-polymers7334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.998, 92.016, 248.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41E
12B
22A
32D
42E
13D
23A
33B
43E
14E
24A
34B
44D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 18
2114B3 - 18
3114D3 - 18
4114E3 - 18
1212A19 - 87
2212B19 - 87
3212D19 - 87
4212E19 - 87
1314A88 - 103
2314B88 - 103
3314D88 - 103
4314E88 - 103
1412A104 - 258
2412B104 - 258
3412D104 - 258
4412E104 - 258
1514A259 - 273
2514B259 - 273
3514D259 - 273
4514E259 - 273
1612A274 - 315
2612B274 - 315
3612D274 - 315
4612E274 - 315
1712A316 - 327
2712B316 - 327
3712D316 - 327
4712E316 - 327
1812A328 - 380
2812B328 - 380
3812D328 - 380
4812E328 - 380
1914A381 - 399
2914B381 - 399
3914D381 - 399
4914E381 - 399
1124B3 - 18
2124A3 - 18
3124D3 - 18
4124E3 - 18
1222B19 - 87
2222A19 - 87
3222D19 - 87
4222E19 - 87
1324B88 - 103
2324A88 - 103
3324D88 - 103
4324E88 - 103
1422B104 - 258
2422A104 - 258
3422D104 - 258
4422E104 - 258
1524B259 - 273
2524A259 - 273
3524D259 - 273
4524E259 - 273
1622B274 - 315
2622A274 - 315
3622D274 - 315
4622E274 - 315
1722B316 - 327
2722A316 - 327
3722D316 - 327
4722E316 - 327
1822B328 - 343
2822A328 - 343
3822D328 - 343
4822E328 - 343
1922B357 - 380
2922A357 - 380
3922D357 - 380
4922E357 - 380
11024B381 - 399
21024A381 - 399
31024D381 - 399
41024E381 - 399
1134D3 - 18
2134A3 - 18
3134B3 - 18
4134E3 - 18
1232D19 - 87
2232A19 - 87
3232B19 - 87
4232E19 - 87
1334D88 - 103
2334A88 - 103
3334B88 - 103
4334E88 - 103
1432D104 - 258
2432A104 - 258
3432B104 - 258
4432E104 - 258
1534D259 - 273
2534A259 - 273
3534B259 - 273
4534E259 - 273
1632D274 - 315
2632A274 - 315
3632B274 - 315
4632E274 - 315
1732D316 - 327
2732A316 - 327
3732B316 - 327
4732E316 - 327
1832D328 - 380
2832A328 - 380
3832B328 - 380
4832E328 - 380
1934D381 - 399
2934A381 - 399
3934B381 - 399
4934E381 - 399
1144E3 - 18
2144A3 - 18
3144B3 - 18
4144D3 - 18
1242E19 - 87
2242A19 - 87
3242B19 - 87
4242D19 - 87
1344E88 - 103
2344A88 - 103
3344B88 - 103
4344D88 - 103
1442E104 - 258
2442A104 - 258
3442B104 - 258
4442D104 - 258
1544E259 - 273
2544A259 - 273
3544B259 - 273
4544D259 - 273
1642E274 - 315
2642A274 - 315
3642B274 - 315
4642D274 - 315
1742E316 - 327
2742A316 - 327
3742B316 - 327
4742D316 - 327
1842E328 - 380
2842A328 - 380
3842B328 - 380
4842D328 - 380
1944E381 - 399
2944A381 - 399
3944B381 - 399
4944D381 - 399

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
5-AMINOLEVULINATE SYNTHASE / 5-AMINOLEVULINIC ACID SYNTHASE / DELTA- AMINOLEVULINATE SYNTHASE / DELTA-ALA SYNTHETASE


Mass: 43673.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM 1710
Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: P18079, 5-aminolevulinate synthase
#2: Chemical
ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDIFFERENT STRAINS OF RHODOBACTER CAPSULATUS

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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: 2.24 Å3/Da / Density % sol: 44.65 %
Crystal growpH: 7.5
Details: 100 MM HEPES PH 7.5, 200 MM NA ACETATE, 8% (V/V) ISOPROPANOL, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2004 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 42365 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 23.864 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2057 4.9 %RANDOM
Rwork0.166 ---
obs0.169 40192 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---2.35 Å20 Å2
3---2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12173 0 92 118 12383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02212540
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.96316991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4551586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28723.291547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.688152023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3771588
X-RAY DIFFRACTIONr_chiral_restr0.1350.21854
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029606
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.26033
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.28567
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.99528101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.046312605
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.61725017
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.76634386
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1324tight positional0.020.05
12B1324tight positional0.020.05
13D1324tight positional0.020.05
14E1324tight positional0.020.05
21B1272tight positional0.020.05
22A1272tight positional0.020.05
23D1272tight positional0.020.05
24E1272tight positional0.020.05
31D1324tight positional0.020.05
32A1324tight positional0.020.05
33B1324tight positional0.020.05
34E1324tight positional0.020.05
41E1324tight positional0.020.05
42A1324tight positional0.020.05
43B1324tight positional0.020.05
44D1324tight positional0.020.05
11A1689medium positional0.440.5
12B1689medium positional0.360.5
13D1689medium positional0.390.5
14E1689medium positional0.420.5
21B1645medium positional0.360.5
22A1645medium positional0.440.5
23D1645medium positional0.390.5
24E1645medium positional0.420.5
31D1689medium positional0.390.5
32A1689medium positional0.440.5
33B1689medium positional0.360.5
34E1689medium positional0.420.5
41E1689medium positional0.420.5
42A1689medium positional0.440.5
43B1689medium positional0.360.5
44D1689medium positional0.390.5
11A1324tight thermal0.030.5
12B1324tight thermal0.030.5
13D1324tight thermal0.030.5
14E1324tight thermal0.030.5
21B1272tight thermal0.030.5
22A1272tight thermal0.030.5
23D1272tight thermal0.030.5
24E1272tight thermal0.030.5
31D1324tight thermal0.030.5
32A1324tight thermal0.030.5
33B1324tight thermal0.030.5
34E1324tight thermal0.030.5
41E1324tight thermal0.030.5
42A1324tight thermal0.030.5
43B1324tight thermal0.030.5
44D1324tight thermal0.030.5
11A1689medium thermal0.382
12B1689medium thermal0.372
13D1689medium thermal0.422
14E1689medium thermal0.42
21B1645medium thermal0.382
22A1645medium thermal0.382
23D1645medium thermal0.422
24E1645medium thermal0.392
31D1689medium thermal0.422
32A1689medium thermal0.382
33B1689medium thermal0.372
34E1689medium thermal0.42
41E1689medium thermal0.42
42A1689medium thermal0.382
43B1689medium thermal0.372
44D1689medium thermal0.422
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 141 -
Rwork0.272 2830 -
obs--93.72 %
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)
11.4507-0.2341-0.10022.9299-1.25434.48320.02860.1107-0.0504-0.00120.1403-0.19270.22520.6809-0.1689-0.10510.07260.01370.3381-0.0519-0.076142.4933.4417.38
21.15990.4773-0.66431.75780.96093.38580.08460.37980.2249-0.1598-0.07630.3303-0.3937-0.78-0.00830.0190.128-0.00440.50930.14550.062515.68611.33810.376
32.3727-1.0154-0.17452.06711.17763.18840.07070.363-0.0663-0.36580.2438-0.11210.1050.3733-0.3145-0.0005-0.02770.01760.44890.0086-0.08538.0612.209-0.659
42.75011.93010.7342.78962.01063.90750.30580.1540.5302-0.2968-0.20670.5825-1.0598-1.1757-0.09920.43240.40290.1690.62650.24090.28089.52928.36524.022
51.17760.0319-1.09092.1854-0.0313.8120.0768-0.05730.12190.47870.13680.0586-0.10870.1797-0.21360.08780.03980.0390.24170.0307-0.026129.710.85634.476
62.6292-1.6656-0.25414.1085-0.22763.87630.3432-0.14450.5430.52270.06620.4647-1.2094-0.6085-0.40950.71940.18490.32840.27560.03970.100916.50432.61241.133
72.84421.5015-2.77253.1059-0.64794.45640.13090.0301-0.29080.87190.0592-0.55070.45280.4218-0.19010.19960.1-0.16150.2782-0.0699-0.057410.648-31.87351.45
80.45220.32610.65542.58980.74732.3978-0.11190.04790.07440.2696-0.09370.3389-0.3494-0.17420.20560.10640.07740.05080.2784-0.0303-0.0261-9.628-12.49645.065
92.1008-0.1914-0.46892.12010.7922.8104-0.0702-0.32390.04751.33340.0883-0.19380.36820.3139-0.01810.66720.0824-0.09880.21990.003-0.10924.087-21.64365.702
101.014-0.51790.30312.4281-0.03222.2581-0.04480.1906-0.0271-0.2583-0.24670.2345-0.2768-0.4830.2914-0.06130.1315-0.04660.4199-0.05040.0266-22.705-20.64428.58
110.92340.03970.17192.07490.6932.06550.10870.29650.02110.0160.0241-0.08060.10080.3168-0.1328-0.00510.10450.0070.3999-0.0238-0.05674.128-31.08929.692
123.1437-0.32260.69920.62920.43592.21280.27520.57560.1621-0.2246-0.36110.37380.0058-0.16210.08590.04370.1433-0.02060.4938-0.1040.0297-18.177-33.69215.746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION2A53 - 296
3X-RAY DIFFRACTION3A297 - 397
4X-RAY DIFFRACTION4B1 - 52
5X-RAY DIFFRACTION5B53 - 296
6X-RAY DIFFRACTION6B297 - 396
7X-RAY DIFFRACTION7D1 - 52
8X-RAY DIFFRACTION8D53 - 296
9X-RAY DIFFRACTION9D297 - 398
10X-RAY DIFFRACTION10E1 - 52
11X-RAY DIFFRACTION11E53 - 296
12X-RAY DIFFRACTION12E297 - 398

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