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- PDB-3ezl: Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 3ezl
TitleCrystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b
ComponentsAcetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / SSGCID / ACETOACETYL-COA REDUCTASE / BURKHOLDERIA PSEUDOMALLEI / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetoacetyl-CoA reductase / acetoacetyl-CoA reductase activity / poly-hydroxybutyrate biosynthetic process / monocarboxylic acid metabolic process / lipid metabolic process / nucleotide binding / cytoplasm
Similarity search - Function
Acetoacetyl-CoA reductase / : / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1710b (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Acetoacetyl-CoA Reductase from Burkholderia Pseudomallei 1710b
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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Assembly

Deposited unit
A: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1232
Polymers27,7991
Non-polymers3241
Water2,450136
1
A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules

A: Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4918
Polymers111,1944
Non-polymers1,2974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area13610 Å2
ΔGint-93 kcal/mol
Surface area34660 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.370, 65.370, 120.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Acetoacetyl-CoA reductase / Acetoacetyl-CoA Reductase


Mass: 27798.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1710b (bacteria)
Strain: 1710B / Gene: phbB-1, BURPS1710b_2329 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JRS9, acetoacetyl-CoA reductase
#2: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PROPLEX-96 A-1: 100MM HEPES PH 7.5, 20% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 12901 / Num. obs: 12901 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Biso Wilson estimate: 32.87 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087
Reflection shellResolution: 2.25→2.31 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.9 / % possible all: 87.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0046refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1i01 modified with ccp4 chainsaw

1i01


Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.492 / SU ML: 0.158 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 637 4.9 %RANDOM
Rwork0.186 ---
all0.189 12901 --
obs0.189 12901 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 13 136 1965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221860
X-RAY DIFFRACTIONr_bond_other_d0.0010.021234
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9372516
X-RAY DIFFRACTIONr_angle_other_deg0.9433004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01724.17779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80815296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8391512
X-RAY DIFFRACTIONr_chiral_restr0.090.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022110
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02381
X-RAY DIFFRACTIONr_mcbond_it0.9261.51190
X-RAY DIFFRACTIONr_mcbond_other0.1991.5509
X-RAY DIFFRACTIONr_mcangle_it1.70721904
X-RAY DIFFRACTIONr_scbond_it2.6273670
X-RAY DIFFRACTIONr_scangle_it4.2684.5612
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 42 -
Rwork0.223 781 -
obs--87.18 %

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