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- PDB-1wmb: Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1wmb
TitleCrystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase
ComponentsD(-)-3-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / NAD / NADH / short chain dehydrogenase
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/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
CACODYLATE ION / D(-)-3-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fragi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crystal 2 MAD PROTOCOL / Resolution: 2 Å
AuthorsIto, K. / Nakajima, Y. / Ichihara, E. / Ogawa, K. / Yoshimoto, T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: d-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi: Molecular Cloning of the Enzyme Gene and Crystal Structure of the Enzyme
Authors: Ito, K. / Nakajima, Y. / Ichihara, E. / Ogawa, K. / Katayama, N. / Nakashima, K. / Yoshimoto, T.
History
DepositionJul 6, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: D(-)-3-hydroxybutyrate dehydrogenase
B: D(-)-3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7476
Polymers53,4252
Non-polymers3234
Water7,710428
1
A: D(-)-3-hydroxybutyrate dehydrogenase
B: D(-)-3-hydroxybutyrate dehydrogenase
hetero molecules

A: D(-)-3-hydroxybutyrate dehydrogenase
B: D(-)-3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,49512
Polymers106,8504
Non-polymers6458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area12990 Å2
ΔGint-78 kcal/mol
Surface area34890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.336, 99.025, 110.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D(-)-3-hydroxybutyrate dehydrogenase


Mass: 26712.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fragi (bacteria) / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5KST5, 3-hydroxybutyrate dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Na cacodylate, PEG3000, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONSPring-8 BL38B120.96400, 0.97986, 0.98012, 1.0000
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 19, 2004
ADSC QUANTUM 42CCDMay 25, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9641
30.979861
40.980121
511
ReflectionResolution: 2→30 Å / Num. all: 47802 / Num. obs: 47802 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.078 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 6880 / Rsym value: 0.306 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Crystal 1 SINGLE WAVELENGTH PROTOCOL, Crystal 2 MAD PROTOCOL
Resolution: 2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2419 -RANDOM
Rwork0.216 ---
all-47737 --
obs-47737 98.9 %-
Displacement parametersBiso mean: 22.4236 Å2
Baniso -1Baniso -2Baniso -3
1-6.202 Å2-8.197 Å21.995 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 12 428 4198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005142
X-RAY DIFFRACTIONc_angle_deg1.18759
X-RAY DIFFRACTIONc_dihedral_angle_d21.30621
X-RAY DIFFRACTIONc_improper_angle_d0.70024
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.278 232 -
Rwork0.239 --
obs-4695 98.9 %

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