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- PDB-2pg0: Crystal structure of acyl-CoA dehydrogenase from Geobacillus kaus... -

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Basic information

Entry
Database: PDB / ID: 2pg0
TitleCrystal structure of acyl-CoA dehydrogenase from Geobacillus kaustophilus
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / GK1316 / Acyl-CoA dehydrogenase / Geobacillus kaustophilus HTA426 / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
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 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 / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChen, L. / Chen, L.-Q. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Li, Y. / Fu, Z.-Q. / Rose, J.P. ...Chen, L. / Chen, L.-Q. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Li, Y. / Fu, Z.-Q. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of acyl-CoA dehydrogenase from G. kaustophilus
Authors: Chen, L. / Chen, L.-Q. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhao, M. / Li, Y. / Fu, Z.-Q. / Rose, J.P. / Wang, B.-C.
History
DepositionApr 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / software
Item: _refine.pdbx_method_to_determine_struct / _software.classification ..._refine.pdbx_method_to_determine_struct / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7474
Polymers87,1762
Non-polymers1,5712
Water10,196566
1
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules

A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,4948
Polymers174,3524
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area20370 Å2
ΔGint-140 kcal/mol
Surface area53370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.276, 119.276, 124.452
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21B-414-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer by the operation -x, -x+y, -z+1/3.

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Components

#1: Protein Acyl-CoA dehydrogenase /


Mass: 43587.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1316 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q5L0D5, EC: 1.3.99.3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: USING 4 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (7.75 mg/ml) AND RESERVOIR SOLUTION CONTAINING 40% v/v MPD, 0.10M CHES (pH 9.4), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionRedundancy: 15.9 % / Av σ(I) over netI: 15.1 / Number: 1496125 / Rmerge(I) obs: 0.097 / Χ2: 1.86 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 94229 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.110.072.73820.5
3.083.8810010.0792.56720.9
2.693.0810010.0942.36719.7
2.442.6910010.1142.05218.1
2.272.4410010.1321.56816.7
2.132.2710010.1771.48915.7
2.032.1310010.2181.20514.9
1.942.0310010.2820.92314
1.861.9499.610.4211.00810.2
1.81.8696.310.4990.8227.3
ReflectionResolution: 1.8→50 Å / Num. obs: 94229 / % possible obs: 99.5 % / Redundancy: 15.9 % / Rsym value: 0.097 / Χ2: 1.857 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.867.30.49990320.822196.3
1.86-1.9410.20.42193511.008199.6
1.94-2.03140.28293930.9231100
2.03-2.1314.90.21893821.2051100
2.13-2.2715.70.17794071.4891100
2.27-2.4416.70.13294121.5681100
2.44-2.6918.10.11494622.0521100
2.69-3.0819.70.09494912.3671100
3.08-3.8820.90.07995412.5671100
3.88-5020.50.0797582.738199.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.42 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4715 5 %RANDOM
Rwork0.205 ---
all0.206 94153 --
obs0.206 94153 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 106 566 6704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226280
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.978504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8735755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35523.724290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1621542
X-RAY DIFFRACTIONr_chiral_restr0.0780.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024722
X-RAY DIFFRACTIONr_nbd_refined0.1970.23125
X-RAY DIFFRACTIONr_nbtor_refined0.30.24328
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2517
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.224
X-RAY DIFFRACTIONr_mcbond_it0.6561.53869
X-RAY DIFFRACTIONr_mcangle_it0.96326020
X-RAY DIFFRACTIONr_scbond_it1.66632915
X-RAY DIFFRACTIONr_scangle_it2.6684.52484
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 347 -
Rwork0.273 6238 -
obs-6585 95.45 %

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