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- PDB-4k6f: X-ray crystal structure of a putative Acetoacetyl-CoA reductase f... -

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Basic information

Entry
Database: PDB / ID: 4k6f
TitleX-ray crystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADP
ComponentsPutative Acetoacetyl-CoA reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Acetoacetyl-CoA reductase
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 / PKS_KR / 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 ...Acetoacetyl-CoA reductase / : / short chain dehydrogenase / PKS_KR / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Acetoacetyl-CoA reductase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (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: X-ray crystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADP
Authors: Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 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_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: Putative Acetoacetyl-CoA reductase
B: Putative Acetoacetyl-CoA reductase
C: Putative Acetoacetyl-CoA reductase
D: Putative Acetoacetyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0167
Polymers109,7864
Non-polymers2,2303
Water17,024945
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-88 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.740, 101.330, 134.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative Acetoacetyl-CoA reductase


Mass: 27446.385 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: phbB, BceJ2315_08230, BCAL0833 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EAU4, acetoacetyl-CoA reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: JCSG+ G4: 0.1 M TRIS-HCl, 200 mM trimethylamine N-oxide, 20% PEG 2000 MME , pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→47.415 Å / Num. all: 146320 / Num. obs: 145003 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.215 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.540.5463.71641151055598.4
1.54-1.580.4474.53627181031798.8
1.58-1.630.3815.25612161003198.8
1.63-1.680.3196.2559752979099.1
1.68-1.730.2757.1357298941698.8
1.73-1.790.2089.0955862920099
1.79-1.860.16711.0553223885499.1
1.86-1.940.13113.2650618857199.3
1.94-2.020.116.6248250825799.3
2.02-2.120.07620.5545258785999.5
2.12-2.240.06124.3143025754299.5
2.24-2.370.05128.3939948711299.6
2.37-2.540.04531.0237307669599.5
2.54-2.740.03935.2434559627299.6
2.74-30.03439.3531552577999.5
3-3.350.02944.6327686525999.5
3.35-3.870.02551.9123914462599.5
3.87-4.740.02456.1620214398099.5
4.74-6.710.02453.8615919312599.3
6.710.02356.18388176497.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6C

4k6c


Resolution: 1.5→47.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 3.217 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 7264 5 %RANDOM
Rwork0.1652 ---
obs0.1676 137740 99.13 %-
all-146320 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.9 Å2 / Biso mean: 15.131 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.38 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 118 945 8215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197463
X-RAY DIFFRACTIONr_bond_other_d0.0010.027111
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.96610186
X-RAY DIFFRACTIONr_angle_other_deg0.811316281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02424.085284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.982151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2161546
X-RAY DIFFRACTIONr_chiral_restr0.080.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
X-RAY DIFFRACTIONr_mcbond_it1.5721.2123921
X-RAY DIFFRACTIONr_mcbond_other1.5721.2123920
X-RAY DIFFRACTIONr_mcangle_it1.8591.8254898
X-RAY DIFFRACTIONr_rigid_bond_restr2.062314574
X-RAY DIFFRACTIONr_sphericity_free32.6685250
X-RAY DIFFRACTIONr_sphericity_bonded7.913515129
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 512 -
Rwork0.23 10031 -
all-10543 -
obs--98.28 %

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