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- PDB-3v2h: The crystal structure of D-beta-hydroxybutyrate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 3v2h
TitleThe crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti
ComponentsD-beta-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / monocarboxylic acid metabolic process / lipid metabolic process
Similarity search - Function
3-hydroxybutyrate dehydrogenase / : / short chain 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...3-hydroxybutyrate dehydrogenase / : / short chain 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-beta-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Zhang, Z. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: The crystal structure of D-beta-hydroxybutyrate dehydrogenase from Sinorhizobium meliloti
Authors: Zhang, Z. / Almo, S.C. / Swaminathan, S.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-beta-hydroxybutyrate dehydrogenase
B: D-beta-hydroxybutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)60,8262
Polymers60,8262
Non-polymers00
Water61334
1
A: D-beta-hydroxybutyrate dehydrogenase
B: D-beta-hydroxybutyrate dehydrogenase

A: D-beta-hydroxybutyrate dehydrogenase
B: D-beta-hydroxybutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)121,6524
Polymers121,6524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11970 Å2
ΔGint-78 kcal/mol
Surface area30170 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-14 kcal/mol
Surface area18480 Å2
MethodPISA
3
A: D-beta-hydroxybutyrate dehydrogenase

A: D-beta-hydroxybutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)60,8262
Polymers60,8262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area18000 Å2
MethodPISA
4
B: D-beta-hydroxybutyrate dehydrogenase

B: D-beta-hydroxybutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)60,8262
Polymers60,8262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3040 Å2
ΔGint-25 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.166, 89.166, 140.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein D-beta-hydroxybutyrate dehydrogenase / BDH / 3-hydroxybutyrate dehydrogenase / 3-HBDH


Mass: 30413.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: bdhA, RB1136, SMb21010 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O86034, 3-hydroxybutyrate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium sulfate, 0.1 M Tris pH5.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 13005 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 55.25 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 18.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 13 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1268 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WMB

1wmb


Resolution: 3→44.583 Å / SU ML: 0.46 / Isotropic thermal model: Isotropic / σ(F): 0.15 / Phase error: 24.55 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 559 4.81 %RANDOM
Rwork0.2261 ---
obs0.229 11613 97.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.611 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5317 Å2-0 Å20 Å2
2---3.5317 Å2-0 Å2
3---7.0633 Å2
Refinement stepCycle: LAST / Resolution: 3→44.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 0 34 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043441
X-RAY DIFFRACTIONf_angle_d0.7334670
X-RAY DIFFRACTIONf_dihedral_angle_d15.7141206
X-RAY DIFFRACTIONf_chiral_restr0.047560
X-RAY DIFFRACTIONf_plane_restr0.003593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.30190.29881430.23392595X-RAY DIFFRACTION95
3.3019-3.77950.27021240.20662731X-RAY DIFFRACTION98
3.7795-4.76090.2871360.1972772X-RAY DIFFRACTION98
4.7609-44.58790.2891560.25592956X-RAY DIFFRACTION99

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