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- PDB-6zzo: Crystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psy... -

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Basic information

Entry
Database: PDB / ID: 6zzo
TitleCrystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psychrobacter arcticus complexed with NAD+ and acetoacetate
ComponentsPutative beta-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / (R)-3-hydroxybutyrate dehydrogenase / psychrophilic enzyme / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity
Similarity search - Function
3-hydroxybutyrate dehydrogenase / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETOACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Putative beta-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 4, 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: Putative beta-hydroxybutyrate dehydrogenase
B: Putative beta-hydroxybutyrate dehydrogenase
C: Putative beta-hydroxybutyrate dehydrogenase
D: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91512
Polymers112,8534
Non-polymers3,0628
Water22,7891265
1
A: Putative beta-hydroxybutyrate dehydrogenase
B: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules

A: Putative beta-hydroxybutyrate dehydrogenase
B: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91512
Polymers112,8534
Non-polymers3,0628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area21290 Å2
ΔGint-118 kcal/mol
Surface area29740 Å2
MethodPISA
2
C: Putative beta-hydroxybutyrate dehydrogenase
D: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules

C: Putative beta-hydroxybutyrate dehydrogenase
D: Putative beta-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91512
Polymers112,8534
Non-polymers3,0628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area21170 Å2
ΔGint-114 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.275, 110.875, 136.903
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-500-

HOH

21C-614-

HOH

31D-678-

HOH

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Components

#1: Protein
Putative beta-hydroxybutyrate dehydrogenase


Mass: 28213.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Gene: Psyc_1428 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4FRT2, 3-hydroxybutyrate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1265 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 45% (v/v) MPD, 0.2 M calcium chloride, 0.1 M Bis Tris

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Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.28→29.51 Å / Num. obs: 266705 / % possible obs: 99.5 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Net I/σ(I): 15.8
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2 / Num. unique obs: 77229 / CC1/2: 0.77 / Rpim(I) all: 0.343 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q2Q

2q2q


Resolution: 1.28→29.51 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.647 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 13358 5 %RANDOM
Rwork0.1424 ---
obs0.1433 253280 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.31 Å2 / Biso mean: 14.224 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.28→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7585 0 232 1311 9128
Biso mean--13.59 28.37 -
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138238
X-RAY DIFFRACTIONr_bond_other_d00.0177708
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6311264
X-RAY DIFFRACTIONr_angle_other_deg1.4381.57417875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47751104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57524.236347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3451525
X-RAY DIFFRACTIONr_chiral_restr0.0750.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.029394
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021577
LS refinement shellResolution: 1.28→1.311 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.271 977 -
Rwork0.263 17729 -
obs--95.11 %

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