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- PDB-5jsc: Crystal structure of a Putative acyl-CoA dehydrogenase from Burkh... -

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Basic information

Entry
Database: PDB / ID: 5jsc
TitleCrystal structure of a Putative acyl-CoA dehydrogenase from Burkholderia xenovorans
ComponentsPutative acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / 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 dehydrogenases signature 1. / 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 acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Putative acyl-CoA dehydrogenase from Burkholderia xenovorans
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Edewards, T.E.
History
DepositionMay 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)179,69925
Polymers175,3024
Non-polymers4,39721
Water31,9591774
1
C: Putative acyl-CoA dehydrogenase
D: Putative acyl-CoA dehydrogenase
hetero molecules

A: Putative acyl-CoA dehydrogenase
B: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,69925
Polymers175,3024
Non-polymers4,39721
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area25220 Å2
ΔGint-282 kcal/mol
Surface area49710 Å2
MethodPISA
2
D: Putative acyl-CoA dehydrogenase
hetero molecules

A: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,70511
Polymers87,6512
Non-polymers2,0549
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7470 Å2
ΔGint-105 kcal/mol
Surface area29760 Å2
MethodPISA
3
A: Putative acyl-CoA dehydrogenase
B: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,60910
Polymers87,6512
Non-polymers1,9588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-62 kcal/mol
Surface area29530 Å2
MethodPISA
4
C: Putative acyl-CoA dehydrogenase
hetero molecules

B: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,99414
Polymers87,6512
Non-polymers2,34312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7970 Å2
ΔGint-138 kcal/mol
Surface area29730 Å2
MethodPISA
5
C: Putative acyl-CoA dehydrogenase
D: Putative acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,09015
Polymers87,6512
Non-polymers2,43913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-136 kcal/mol
Surface area29090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.300, 73.750, 149.490
Angle α, β, γ (deg.)90.000, 99.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative acyl-CoA dehydrogenase /


Mass: 43825.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_B0278 / Plasmid: BuxeA.00027.j.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13JS1, Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor

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Non-polymers , 5 types, 1795 molecules

#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1774 / 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: 2.43 Å3/Da / Density % sol: 49 % / Mosaicity: 0.15 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: RigakuReagents JCSG+ screen A6: 20% PEG 1000, 200mM Li2SO4, 50mM Na2HPO4/Citric acid pH4.2; BuxeA.00027.j.B1.PS37826 at 15mg/ml + 2.5mM CoA; cryo: 15% EG + 1mM CoA in 2 steps; tray 270711a6; puck vod9-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 25, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 266729 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 14.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.98
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.540.5282.19194.5
1.54-1.580.4283.12199.8
1.58-1.630.3573.871100
1.63-1.680.34.611100
1.68-1.730.2395.79199.9
1.73-1.790.1957.1199.9
1.79-1.860.1548.871100
1.86-1.940.12311.081100
1.94-2.020.09613.97199.9
2.02-2.120.0816.84199.9
2.12-2.240.06619.961100
2.24-2.370.05722.74199.9
2.37-2.540.05324.57199.9
2.54-2.740.04727.08199.9
2.74-30.04229.95199.9
3-3.350.03833.24199.8
3.35-3.870.03536.4199.7
3.87-4.740.03138.52199.7
4.74-6.710.03137.9199.7
6.710.02938.66197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
PHENIXdev_2386refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5idu

5idu


Resolution: 1.5→45.004 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.34
RfactorNum. reflection% reflection
Rfree0.1601 1958 0.73 %
Rwork0.1298 --
obs0.13 266691 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.45 Å2 / Biso mean: 20.6833 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.5→45.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11493 0 277 1791 13561
Biso mean--19.5 34.29 -
Num. residues----1551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512360
X-RAY DIFFRACTIONf_angle_d0.79816868
X-RAY DIFFRACTIONf_chiral_restr0.0471878
X-RAY DIFFRACTIONf_plane_restr0.0052329
X-RAY DIFFRACTIONf_dihedral_angle_d14.367435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53760.25211370.1945178781801594
1.5376-1.57910.21431340.16161883418968100
1.5791-1.62560.191390.14621889819037100
1.6256-1.67810.18561670.13331893319100100
1.6781-1.73810.151300.1231895219082100
1.7381-1.80760.18961240.11831889019014100
1.8076-1.88990.15641270.11691901519142100
1.8899-1.98960.16431480.1161897819126100
1.9896-2.11420.1291430.11391897519118100
2.1142-2.27740.15491370.11241892419061100
2.2774-2.50660.13321420.12361901819160100
2.5066-2.86930.16781350.13241904419179100
2.8693-3.61470.16171410.13741911119252100
3.6147-45.02410.15241540.1343192831943799

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