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- PDB-7lnm: Ornithine Aminotransferase (OAT) cocrystallized with its inactiva... -

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Basic information

Entry
Database: PDB / ID: 7lnm
TitleOrnithine Aminotransferase (OAT) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(difluoromethylene)cyclopentene-1-carboxylic acid
ComponentsOrnithine aminotransferase, mitochondrial
KeywordsTRANSFERASE/Inactivator / Ornithine Aminotransferase / OAT / aminotransferase / inactivator / inhibitor / TRANSFERASE / TRANSFERASE-Inactivator complex
Function / homology
Function and homology information


arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-Y7S / Ornithine aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsButrin, A. / Catlin, D. / Zhu, W. / Liu, D. / Silverman, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Remarkable and Unexpected Mechanism for ( S )-3-Amino-4-(difluoromethylenyl)cyclohex-1-ene-1-carboxylic Acid as a Selective Inactivator of Human Ornithine Aminotransferase.
Authors: Zhu, W. / Doubleday, P.F. / Butrin, A. / Weerawarna, P.M. / Melani, R.D. / Catlin, D.S. / Dwight, T.A. / Liu, D. / Kelleher, N.L. / Silverman, R.B.
History
DepositionFeb 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
E: Ornithine aminotransferase, mitochondrial
F: Ornithine aminotransferase, mitochondrial
I: Ornithine aminotransferase, mitochondrial
J: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,39612
Polymers269,1626
Non-polymers2,2346
Water30,4451690
1
B: Ornithine aminotransferase, mitochondrial
C: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4654
Polymers89,7212
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-61 kcal/mol
Surface area26020 Å2
MethodPISA
2
E: Ornithine aminotransferase, mitochondrial
F: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4654
Polymers89,7212
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-61 kcal/mol
Surface area26090 Å2
MethodPISA
3
I: Ornithine aminotransferase, mitochondrial
J: Ornithine aminotransferase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4654
Polymers89,7212
Non-polymers7452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-58 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.720, 115.720, 188.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase


Mass: 44860.320 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical
ChemComp-Y7S / (1~{R},3~{S},4~{R})-3-methyl-4-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]cyclopentane-1-carboxylic acid


Mass: 372.310 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H21N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1690 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed ...Details: The freshly prepared enzyme was buffer exchanged into 50 mM Tricine pH 7.8 and concentrated to a protein concentration of 6 mg/mL. For each hanging drop, 2 ul of protein solution was mixed with equal volume of well solution and 0.5 ul of 10 mM compound. The crystals with the best morphology and size grew in a final condition containing 12% PEG 8000, 200 mM NaCl, 10% glycerol, 50 mM Tricine pH 7.8.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→68.56 Å / Num. obs: 190270 / % possible obs: 100 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.068 / Rrim(I) all: 0.136 / Net I/σ(I): 4.6 / Num. measured all: 749788 / Scaling rejects: 842
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.033.51.0863303593770.3760.6781.2841.3100
10.95-68.563.70.07422411360.9870.0420.0827.697.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OAT
Resolution: 2→36.48 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 9669 5.08 %
Rwork0.158 --
obs0.159 190160 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.9 Å2
Refinement stepCycle: LAST / Resolution: 2→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18938 0 150 1690 20778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.34173180.27666010X-RAY DIFFRACTION100
2.02-2.050.2763800.25185975X-RAY DIFFRACTION100
2.05-2.070.29422940.24696077X-RAY DIFFRACTION100
2.07-2.10.28423280.23546002X-RAY DIFFRACTION100
2.1-2.130.25463140.22095998X-RAY DIFFRACTION100
2.13-2.150.24423120.20466014X-RAY DIFFRACTION100
2.15-2.190.22413260.20336066X-RAY DIFFRACTION100
2.19-2.220.24343480.19395954X-RAY DIFFRACTION100
2.22-2.250.20522800.18976081X-RAY DIFFRACTION100
2.25-2.290.23412560.18796023X-RAY DIFFRACTION100
2.29-2.330.21333460.18286032X-RAY DIFFRACTION100
2.33-2.370.21453660.17756009X-RAY DIFFRACTION100
2.37-2.420.21122880.17246005X-RAY DIFFRACTION100
2.42-2.470.23823000.17546049X-RAY DIFFRACTION100
2.47-2.520.19783720.1665945X-RAY DIFFRACTION100
2.52-2.580.20692700.17296107X-RAY DIFFRACTION100
2.58-2.640.21953450.17226016X-RAY DIFFRACTION100
2.64-2.710.20383520.16465951X-RAY DIFFRACTION100
2.71-2.790.22192820.16446031X-RAY DIFFRACTION100
2.79-2.880.22252780.16386068X-RAY DIFFRACTION100
2.88-2.990.22293280.16196083X-RAY DIFFRACTION100
2.99-3.110.19683000.15846004X-RAY DIFFRACTION100
3.11-3.250.17013360.15946016X-RAY DIFFRACTION100
3.25-3.420.17513300.15886015X-RAY DIFFRACTION100
3.42-3.630.17413520.14336002X-RAY DIFFRACTION100
3.63-3.910.14473440.12875956X-RAY DIFFRACTION100
3.91-4.310.15523320.11926033X-RAY DIFFRACTION100
4.31-4.930.12223390.10935996X-RAY DIFFRACTION100
4.93-6.20.14413060.13736037X-RAY DIFFRACTION100
6.21-36.480.15393470.13985936X-RAY DIFFRACTION99
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)
11.32922.16110.40513.60110.42230.84660.0172-0.1066-0.44740.0898-0.0567-0.04190.70480.17850.0080.68210.08570.03030.25710.0630.3397-6.9992-15.311210.8101
21.15050.55090.21681.966-0.24670.51880.12740.0901-0.2229-0.0257-0.0729-0.14940.40050.3904-0.01670.50740.1770.01010.3261-0.00240.21566.7104-7.7506-9.7311
31.5372-0.32140.51730.10790.13322.7985-0.00290.010.1101-0.0255-0.0750.016-0.00660.19880.07130.29530.0102-0.02020.10570.02940.1779-8.522915.9029-5.2873
43.48220.73130.32273.00160.75621.39370.0340.1754-0.1667-0.1958-0.12590.05060.15580.1270.09430.37380.05-0.03120.14720.01350.1595-11.006312.6076-16.4879
51.59830.07160.34261.27-0.96562.16120.0220.0672-0.0199-0.0531-0.0939-0.09340.13780.33140.0840.37860.09550.01290.20450.01180.17161.81634.8757-13.5328
63.63420.98231.03872.03550.34691.8525-0.06250.0667-0.1806-0.14010.0670.33380.4413-0.02180.00370.52070.0762-0.01250.12140.03660.2589-12.4366-9.9278-15.6334
74.16760.8034-1.66920.413-1.18824.07480.1569-0.0829-0.24740.06620.04130.21770.3361-0.252-0.17760.5829-0.0023-0.03820.16010.03030.3469-16.9168-17.2496-9.0128
82.3441-1.30931.25612.1595-1.51041.48850.06120.24960.2028-0.3369-0.1221-0.42230.31390.75340.04940.35970.12810.05920.67230.0220.353825.35983.1124-5.4315
91.1035-0.2908-0.19091.14350.32291.5289-0.0034-0.134-0.04560.05560.0285-0.04380.13340.4193-0.02990.32110.0489-0.01360.28210.04760.1524.56785.974514.3719
104.09380.11970.91662.12070.67711.6954-0.0016-0.23220.20310.09840.1245-0.49160.14880.7762-0.12310.36730.09510.01290.63030.00780.23221.67124.500812.7882
110.86592.0446-0.1475.3638-1.64523.1804-0.1413-0.09750.21210.02520.1633-0.8535-0.08830.8062-0.00790.27470.07680.01390.9414-0.01840.573433.46079.13776.4908
120.915-1.6249-0.32943.62430.62840.29810.06840.15650.4377-0.045-0.05640.0249-0.72350.1247-0.02780.7321-0.0692-0.01110.27740.0860.351950.9034-18.0576-30.8438
131.442-1.39050.08252.3698-0.45980.73430.13440.03340.2874-0.1394-0.03450.0879-0.37740.253-0.0610.6518-0.17830.040.2370.00220.299358.2055-16.1784-12.3808
144.31410.1075-1.48241.9156-0.06262.4060.1318-0.17030.11990.1936-0.0326-0.3885-0.36750.6646-0.11350.3757-0.147-0.05910.43090.04130.235972.0775-36.7611-7.268
151.44880.3115-0.50340.120.18482.6053-0.0170-0.13410.0118-0.07250.03840.00660.19470.08730.3176-0.01530.01980.10660.03020.193549.3386-49.3237-14.4626
163.6241-0.9464-0.17082.98920.88041.46920.0183-0.16150.15380.1865-0.1575-0.0019-0.11190.09380.13830.3731-0.05070.02880.14480.0170.163546.8966-45.9574-3.4149
171.52620.0859-0.12791.3115-1.07482.0150.0378-0.0247-0.0078-0.0087-0.1036-0.1344-0.13420.32210.07740.3825-0.0987-0.01380.20470.00910.167459.693-38.3028-6.2298
183.3001-0.7168-1.05371.93950.33811.7495-0.0184-0.06110.18240.10880.05520.3039-0.4412-0.0088-0.0240.5409-0.08060.00740.12910.04260.247745.4451-23.4679-4.1579
194.0607-0.98491.44650.6595-1.53283.85570.20830.06140.2667-0.06070.0480.2283-0.2719-0.2632-0.23460.6094-0.01360.0450.16480.03520.360940.9624-16.1686-10.7403
208.57050.0482-1.49564.7246-0.90495.3243-0.0236-0.70170.06820.6445-0.0755-0.7643-0.29260.89140.07630.4021-0.0413-0.11450.60470.08110.386580.4092-42.5203-6.1801
211.7432-0.0691-0.16051.17840.23810.9210.0488-0.01180.223-0.03420.0152-0.2027-0.38310.5005-0.04690.454-0.21070.01820.43160.03360.255372.0984-26.1447-24.526
222.6860.271-0.40221.4954-0.48212.3909-0.00690.1238-0.1929-0.01790.0223-0.04890.18440.3734-0.01750.31410.00570.00990.19720.00590.14760.4212-48.7286-36.1495
233.02550.3247-0.26621.64910.54721.972-0.01760.2889-0.141-0.10480.0813-0.2609-0.19250.7233-0.07020.3553-0.10170.01550.47390.04520.214374.2838-36.4566-33.8169
241.1824-1.85530.12675.1677-1.74913.5107-0.00760.0583-0.2799-0.05080.2037-0.68040.08480.83-0.1590.2888-0.084-0.02630.9841-0.04710.577991.3328-42.5186-26.2039
250.8017-0.86740.16270.9278-0.17820.0341-0.0541-0.2441-0.01660.41860.42990.5983-0.3248-0.636-0.21230.5590.25410.27830.5660.24760.8044-54.682449.16643.5494
260.4436-0.1462-0.49720.7583-0.10951.21680.0160.0845-0.0146-0.09780.30040.62530.0044-0.6476-0.28020.3319-0.0523-0.13130.45890.24950.6945-53.432534.0714-20.3857
270.60580.03920.28180.5328-0.8621.70560.01950.01290.07250.03840.05940.1978-0.061-0.0459-0.08110.27720.0079-0.00480.09760.02530.25-26.824540.6678-16.865
282.8071-1.1852-0.42182.48920.36650.8607-0.0480.07140.238-0.12150.13790.3621-0.1261-0.1927-0.0980.30480.0177-0.0440.1760.08830.331-35.622748.2386-25.507
291.6914-0.8606-0.283.0549-0.0871.33060.0633-0.03290.1630.01450.29920.4005-0.2909-0.446-0.25370.31180.07770.03390.30220.17290.4554-46.739948.9706-17.3854
300.0562-0.1228-0.0871.17010.25390.44120.07120.0290.21150.24850.11140.1715-0.3556-0.27080.02520.66880.42080.25460.36530.25990.7837-51.412962.5281-6.1185
310.29420.4203-0.27390.6148-0.44870.58210.0160.1201-0.0627-0.27590.38350.57860.276-0.6684-0.29330.4591-0.1816-0.19610.55810.27830.8305-56.132420.1948-17.6166
320.6824-0.0823-0.09160.9198-0.48541.28830.034-0.0378-0.00050.05660.12450.34-0.0732-0.2139-0.14210.27470.00480.04390.13390.06050.3168-34.36629.6985-0.5062
332.40341.05850.30942.4230.1270.959-0.0236-0.0751-0.21470.11120.14820.39410.1158-0.2045-0.13020.3004-0.02060.04590.16650.08740.3396-35.627718.48585.8418
341.66010.79020.28783.3195-0.11391.350.07780.036-0.1399-0.05390.26620.38740.2916-0.4429-0.24510.3046-0.0769-0.03090.30790.16710.451-46.691217.7058-2.4701
350.03580.05920.07381.03270.23660.42880.1298-0.0542-0.186-0.21830.13180.12410.3565-0.26240.00510.6876-0.4557-0.26170.33830.26480.7898-51.23184.4564-13.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 36 THROUGH 61 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 62 THROUGH 141 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 142 THROUGH 220 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 221 THROUGH 263 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 264 THROUGH 326 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 327 THROUGH 389 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 390 THROUGH 439 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 36 THROUGH 94 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 95 THROUGH 313 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 314 THROUGH 389 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 390 THROUGH 439 )
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 36 THROUGH 61 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 62 THROUGH 105 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 106 THROUGH 141 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 142 THROUGH 220 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 221 THROUGH 263 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 264 THROUGH 326 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 327 THROUGH 389 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 390 THROUGH 439 )
20X-RAY DIFFRACTION20CHAIN 'F' AND (RESID 36 THROUGH 61 )
21X-RAY DIFFRACTION21CHAIN 'F' AND (RESID 62 THROUGH 141 )
22X-RAY DIFFRACTION22CHAIN 'F' AND (RESID 142 THROUGH 263 )
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESID 264 THROUGH 389 )
24X-RAY DIFFRACTION24CHAIN 'F' AND (RESID 390 THROUGH 439 )
25X-RAY DIFFRACTION25CHAIN 'I' AND (RESID 36 THROUGH 82 )
26X-RAY DIFFRACTION26CHAIN 'I' AND (RESID 83 THROUGH 141 )
27X-RAY DIFFRACTION27CHAIN 'I' AND (RESID 142 THROUGH 220 )
28X-RAY DIFFRACTION28CHAIN 'I' AND (RESID 221 THROUGH 290 )
29X-RAY DIFFRACTION29CHAIN 'I' AND (RESID 291 THROUGH 389 )
30X-RAY DIFFRACTION30CHAIN 'I' AND (RESID 390 THROUGH 439 )
31X-RAY DIFFRACTION31CHAIN 'J' AND (RESID 36 THROUGH 106 )
32X-RAY DIFFRACTION32CHAIN 'J' AND (RESID 107 THROUGH 220 )
33X-RAY DIFFRACTION33CHAIN 'J' AND (RESID 221 THROUGH 290 )
34X-RAY DIFFRACTION34CHAIN 'J' AND (RESID 291 THROUGH 389 )
35X-RAY DIFFRACTION35CHAIN 'J' AND (RESID 390 THROUGH 439 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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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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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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