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- PDB-6zzq: Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Aci... -

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Basic information

Entry
Database: PDB / ID: 6zzq
TitleCrystal structure of (R)-3-hydroxybutyrate dehydrogenase from Acinetobacter baumannii complexed with NAD+ and acetoacetate
Components3-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / (R)-3-hydroxybutyrate dehydrogenase / short-chain dehydrogenase/reductase / mesophilic enzyme
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase activity
Similarity search - Function
3-hydroxybutyrate dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETOACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMachado, T.F.G. / da Silva, R.G. / Gloster, T.M. / McMahon, S.A. / Oehler, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Dissecting the Mechanism of ( R )-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry.
Authors: Machado, T.F.G. / Purg, M. / McMahon, S.A. / Read, B.J. / Oehler, V. / Aqvist, J. / Gloster, T.M. / da Silva, R.G.
History
DepositionAug 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4354
Polymers27,5681
Non-polymers8683
Water2,180121
1
A: 3-hydroxybutyrate dehydrogenase
hetero molecules

A: 3-hydroxybutyrate dehydrogenase
hetero molecules

A: 3-hydroxybutyrate dehydrogenase
hetero molecules

A: 3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,74216
Polymers110,2714
Non-polymers3,47012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation7_645y+1,x-1,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area19460 Å2
ΔGint-51 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.348, 64.348, 194.513
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-497-

HOH

31A-516-

HOH

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Components

#1: Protein 3-hydroxybutyrate dehydrogenase /


Mass: 27567.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: A7M79_09600, BGC29_06470 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A1E3M3N6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15% (v/w) PEG 3350, 0.1 M succinic acid

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Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.93→53.57 Å / Num. obs: 18880 / % possible obs: 100 % / Redundancy: 24.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.029 / Rrim(I) all: 0.144 / Net I/σ(I): 15.7
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 16.7 % / Rmerge(I) obs: 3.014 / Num. unique obs: 1344 / CC1/2: 0.827 / R split: 1.6 / Rpim(I) all: 0.759 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V2H

2v2h


Resolution: 1.93→53.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.279 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 876 4.9 %RANDOM
Rwork0.2087 ---
obs0.2117 16971 94.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.55 Å2 / Biso mean: 33.566 Å2 / Biso min: 16.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 1.93→53.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 58 123 2064
Biso mean--43.82 41.11 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171856
X-RAY DIFFRACTIONr_angle_refined_deg1.481.6332671
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5734295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14924.65873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57615317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.173155
X-RAY DIFFRACTIONr_chiral_restr0.070.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022227
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 1.931→1.981 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 70 -
Rwork0.366 1213 -
all-1283 -
obs--95.82 %

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