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- PDB-3vdr: Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared ... -

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Basic information

Entry
Database: PDB / ID: 3vdr
TitleCrystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)
ComponentsD-3-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / NAD DEPENDENT ENZYMES / KETONE BODIES
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding / metal ion 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(3R)-3-hydroxybutanoic acid / ACETOACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHoque, M.M. / Shimizu, S. / Juan, E.C.M. / Sato, Y. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Amano, H. / Suzuki, K. / Sekiguchi, T. ...Hoque, M.M. / Shimizu, S. / Juan, E.C.M. / Sato, Y. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Amano, H. / Suzuki, K. / Sekiguchi, T. / Tsunoda, M. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.
Authors: Hoque, M.M. / Shimizu, S. / Juan, E.C.M. / Sato, Y. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Amano, H. / Sekiguchi, T. / Tsunoda, M. / Takenaka, A.
History
DepositionJan 6, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 8, 2012ID: 3EEW
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: D-3-hydroxybutyrate dehydrogenase
B: D-3-hydroxybutyrate dehydrogenase
C: D-3-hydroxybutyrate dehydrogenase
D: D-3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,80325
Polymers108,4764
Non-polymers6,32721
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-174 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.100, 91.100, 262.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-3-hydroxybutyrate dehydrogenase


Mass: 27118.943 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria)
References: UniProt: D0VWQ0, 3-hydroxybutyrate dehydrogenase

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Non-polymers , 7 types, 265 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Chemical
ChemComp-3HR / (3R)-3-hydroxybutanoic acid


Mass: 104.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O3
#7: Chemical
ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNAI AND NAD ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. AAE AND 3HR ARE IN ALTERNATE ...NAI AND NAD ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. AAE AND 3HR ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG, 5MM NAD+, 200MM 3-HYDROXYBUTYRATE SODIUM SALT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 26, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 20947 / % possible obs: 91.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 26.9
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 9.48 / % possible all: 96.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.2refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YZ7

2yz7


Resolution: 3→43 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 2062 -RANDOM
Rwork0.1761 ---
all-20936 --
obs-18874 91 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.491 Å20 Å20 Å2
2---0.491 Å20 Å2
3---0.981 Å2
Refinement stepCycle: LAST / Resolution: 3→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7624 0 413 244 8281
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.02 / % reflection obs: 94.9 %

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