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

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Basic information

Entry
Database: PDB / ID: 6zzp
TitleCrystal structure of (R)-3-hydroxybutyrate dehydrogenase from Psychrobacter arcticus complexed with NAD+ and 3-oxovalerate
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 / nucleotide binding
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-oxidanylidenepentanoic acid / Putative beta-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPsychrobacter arcticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.2May 1, 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)115,97212
Polymers112,8534
Non-polymers3,1188
Water17,907994
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)115,97212
Polymers112,8534
Non-polymers3,1188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area19900 Å2
ΔGint-133 kcal/mol
Surface area31710 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)115,97212
Polymers112,8534
Non-polymers3,1188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area19910 Å2
ΔGint-135 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.753, 111.132, 137.300
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
11A-503-

HOH

21A-580-

HOH

31B-567-

HOH

41B-597-

HOH

51B-631-

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


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-QT8 / 3-oxidanylidenepentanoic acid / 3-oxovalerate


Mass: 116.115 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 994 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.18 M succinic acid, 17.2% PEG 3350

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Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→29.64 Å / Num. obs: 90721 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.057 / Net I/σ(I): 12
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 24677 / CC1/2: 0.738 / Rpim(I) all: 0.406 / % possible all: 89.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292104350

Resolution: 1.84→29.64 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.886 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 4528 5 %RANDOM
Rwork0.1457 ---
obs0.1479 86146 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.59 Å2 / Biso mean: 20.873 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2---1.15 Å20 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 1.84→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7500 0 216 1022 8738
Biso mean--23.51 32.58 -
Num. residues----1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177457
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.63110889
X-RAY DIFFRACTIONr_angle_other_deg1.4151.58217256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7251047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38124.268328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.435151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5561522
X-RAY DIFFRACTIONr_chiral_restr0.070.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029034
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021524
LS refinement shellResolution: 1.845→1.893 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 294 -
Rwork0.238 5897 -
all-6191 -
obs--93.1 %

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