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- PDB-4kto: Crystal Structure Of a Putative Isovaleryl-CoA dehydrogenase (PSI... -

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Basic information

Entry
Database: PDB / ID: 4kto
TitleCrystal Structure Of a Putative Isovaleryl-CoA dehydrogenase (PSI-NYSGRC-012251) from Sinorhizobium meliloti 1021
Componentsisovaleryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / isovaleryl-coA / dehydrogenase / Protein structure initiative / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium (NYSGRC)
Function / homology
Function and homology information


isovaleryl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal ...Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putative isovaleryl-CoA dehydrogenase protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.137 Å
AuthorsKumar, P.R. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Glenn, A.S. / Hammonds, J. / Hillerich, B. ...Kumar, P.R. / Ahmed, M. / Attonito, J. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Himmel, D. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Wasserman, S.R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a Putative Isovaleryl-CoA dehydrogenase from Sinorhizobium meliloti 1021
Authors: Kumar, P.R. / Hillerich, B. / Love, J. / Seidel, R. / Almo, S.C.
History
DepositionMay 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: isovaleryl-CoA dehydrogenase
B: isovaleryl-CoA dehydrogenase
C: isovaleryl-CoA dehydrogenase
D: isovaleryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,49811
Polymers178,9894
Non-polymers3,5097
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22030 Å2
ΔGint-135 kcal/mol
Surface area47590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.912, 115.158, 143.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a Tetramer

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Components

#1: Protein
isovaleryl-CoA dehydrogenase /


Mass: 44747.242 Da / Num. of mol.: 4 / Mutation: V154D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: ivdH, SM_b21121 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92VK1, isovaleryl-CoA dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT); Reservoir (0.17M Sodium Acetate, 0.085M Tris, 25.5% PEG4000, 15% (v/v) Glycerol)pH 8.5 - MCSG1 #20); Cryoprotection ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT); Reservoir (0.17M Sodium Acetate, 0.085M Tris, 25.5% PEG4000, 15% (v/v) Glycerol)pH 8.5 - MCSG1 #20); Cryoprotection (Paratone-N), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 18, 2013 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.137→50 Å / Num. all: 81914 / Num. obs: 79333 / % possible obs: 96.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 18.09
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.15-2.195.2196.4
2.19-2.235.31960.884
2.23-2.275.4195.70.751
2.27-2.325.5195.80.701
2.32-2.375.61960.607
2.37-2.425.8195.90.53
2.42-2.485.9196.30.447
2.48-2.556196.30.404
2.55-2.626.2196.40.358
2.62-2.716.4196.20.311
2.71-2.816.5196.40.262
2.81-2.926.6196.10.222
2.92-3.056.6196.60.197
3.05-3.216.6196.20.164
3.21-3.416.4196.40.138
3.41-3.686.21970.112
3.68-4.056.1199.10.09
4.05-4.636.7199.80.071
4.63-5.837.311000.068
5.83-506.8198.50.06

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1IVH
Resolution: 2.137→31.776 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 1.33 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 3972 5.02 %
Rwork0.175 --
obs0.1776 79155 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.4151 Å2
Refinement stepCycle: LAST / Resolution: 2.137→31.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11229 0 236 566 12031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811654
X-RAY DIFFRACTIONf_angle_d1.19815743
X-RAY DIFFRACTIONf_dihedral_angle_d14.7434293
X-RAY DIFFRACTIONf_chiral_restr0.0771723
X-RAY DIFFRACTIONf_plane_restr0.0052028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1369-2.1630.3038720.24871421X-RAY DIFFRACTION51
2.163-2.19030.36661440.2332656X-RAY DIFFRACTION95
2.1903-2.21920.26761450.22722681X-RAY DIFFRACTION97
2.2192-2.24960.27851520.21432665X-RAY DIFFRACTION95
2.2496-2.28170.25241280.21582662X-RAY DIFFRACTION96
2.2817-2.31570.28291550.20422659X-RAY DIFFRACTION96
2.3157-2.35190.29291700.20782649X-RAY DIFFRACTION96
2.3519-2.39040.27311210.19452688X-RAY DIFFRACTION96
2.3904-2.43170.26021320.1892705X-RAY DIFFRACTION96
2.4317-2.47590.23581400.17582670X-RAY DIFFRACTION96
2.4759-2.52350.25361600.18442686X-RAY DIFFRACTION96
2.5235-2.57490.27261410.18242692X-RAY DIFFRACTION96
2.5749-2.63090.26911340.1752691X-RAY DIFFRACTION96
2.6309-2.69210.25351400.17142702X-RAY DIFFRACTION96
2.6921-2.75940.2341330.16512706X-RAY DIFFRACTION96
2.7594-2.83390.20741490.16272702X-RAY DIFFRACTION96
2.8339-2.91730.23031160.16132749X-RAY DIFFRACTION96
2.9173-3.01140.20881530.17382686X-RAY DIFFRACTION96
3.0114-3.11890.23041380.16822714X-RAY DIFFRACTION96
3.1189-3.24360.18451540.16932703X-RAY DIFFRACTION96
3.2436-3.39110.22621430.16662730X-RAY DIFFRACTION96
3.3911-3.56970.23671480.15972719X-RAY DIFFRACTION96
3.5697-3.7930.20421390.15442795X-RAY DIFFRACTION98
3.793-4.08530.18031430.14752838X-RAY DIFFRACTION99
4.0853-4.49540.19711470.14872850X-RAY DIFFRACTION100
4.4954-5.14350.19111560.15722862X-RAY DIFFRACTION100
5.1435-6.47130.21971630.19882898X-RAY DIFFRACTION100
6.4713-31.780.2331560.20233004X-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)
13.7528-0.314-0.28862.20431.35012.11230.00960.037-0.69180.10040.01570.12110.828-0.0619-0.03050.34020.01-0.05560.2010.02940.29186.553441.9289107.3288
22.21741.276-0.04392.7739-0.28051.2929-0.0145-0.1320.21920.1202-0.01760.0946-0.11610.04590.02310.18380.0163-0.05890.223600.143992.082365.3542114.0754
34.49762.60190.27443.31860.40050.8739-0.0094-0.14170.29530.0652-0.06440.0259-0.0620.02620.07090.22580.0431-0.0620.150.04380.100285.419665.4331111.6327
42.2733-0.487-0.9650.9372-0.06792.2149-0.11060.0031-0.1596-0.12830.03710.08890.136-0.01520.0270.18330.0007-0.04590.1624-0.00190.1573.766354.486100.5477
53.4116-0.12723.13472.15061.17626.3114-0.0040.18090.46580.0033-0.0432-0.1785-0.1660.70690.11260.1466-0.03320.02690.3382-0.0040.231391.210952.329276.1846
61.20410.03430.0023.6786-0.07881.54830.02580.0986-0.279-0.0642-0.07440.26960.3610.09760.04460.2750.07480.01680.2258-0.04020.222676.664433.318469.0243
71.1587-0.23830.40715.48621.38881.735-0.07190.1075-0.30610.10350.03840.26120.26620.05290.04070.19080.00870.08130.2287-0.02310.195772.332838.312571.5921
81.156-0.59660.30450.3756-0.09751.6557-0.02010.10510.0338-0.0314-0.032-0.02160.04830.06140.06740.20750.0166-0.02040.2042-0.02040.168373.126552.466483.7876
93.1145-0.88140.73841.6251-0.76747.9695-0.13560.07090.6219-0.0013-0.0364-0.1053-0.6997-0.33240.15870.26970.1110.01430.18370.02930.265643.836378.0072106.0925
102.75331.0762-0.572.5553-0.99612.2104-0.0676-0.0653-0.2970.0460.17720.20860.2471-0.4507-0.07990.1946-0.00890.01640.33060.03360.238539.939756.311118.1583
113.34351.2522-1.49032.5629-1.8732.2936-0.14120.0274-0.3724-0.11940.10770.15960.2337-0.3670.00540.2557-0.02490.01840.2195-0.03340.202145.988455.7977115.2253
122.70380.19660.72840.47710.06892.2635-0.08230.1208-0.0463-0.12980.00130.04730.0402-0.16950.07460.1910.01730.01780.2063-0.01050.144854.397962.4952100.2731
130.8477-1.48170.35092.9948-1.67966.6922-0.0050.0579-0.4535-0.0733-0.10060.50480.2465-0.62740.0930.2269-0.0345-0.05720.4956-0.0680.28736.127862.202277.9407
142.10390.1663-0.3522.2787-0.27792.26260.07260.24550.3187-0.12750.00480.0105-0.5485-0.3597-0.04070.35640.1713-0.02820.32790.03820.211549.642879.282266.0579
151.3048-0.0623-0.36424.0611-1.18532.2675-0.00570.14810.1910.0394-0.0859-0.1065-0.5006-0.33240.04860.25140.0849-0.09710.2783-0.0240.194654.364474.937169.263
162.282-0.9054-0.74981.21870.79933.23280.0392-0.0191-0.170.0279-0.09850.11340.1523-0.16030.03520.1840.0229-0.03560.21830.02470.135254.545661.114483.3574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 192 )
3X-RAY DIFFRACTION3chain 'A' and (resid 193 through 272 )
4X-RAY DIFFRACTION4chain 'A' and (resid 273 through 387 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 27 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 192 )
7X-RAY DIFFRACTION7chain 'B' and (resid 193 through 272 )
8X-RAY DIFFRACTION8chain 'B' and (resid 273 through 387 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 27 )
10X-RAY DIFFRACTION10chain 'C' and (resid 28 through 192 )
11X-RAY DIFFRACTION11chain 'C' and (resid 193 through 272 )
12X-RAY DIFFRACTION12chain 'C' and (resid 273 through 387 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 27 )
14X-RAY DIFFRACTION14chain 'D' and (resid 28 through 192 )
15X-RAY DIFFRACTION15chain 'D' and (resid 193 through 272 )
16X-RAY DIFFRACTION16chain 'D' and (resid 273 through 387 )

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