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- PDB-2ztu: T190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+ -

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Basic information

Entry
Database: PDB / ID: 2ztu
TitleT190A mutant of D-3-hydroxybutyrate dehydrogenase complexed with NAD+
ComponentsD(-)-3-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductase / SDR family / NAD / NADH / HBDH
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / monocarboxylic acid metabolic process / lipid metabolic process / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D(-)-3-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fragi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsNakashima, K. / Nakajima, Y. / Ito, K. / Yoshimoto, T.
CitationJournal: J.Biochem. / Year: 2009
Title: Closed complex of the D-3-hydroxybutyrate dehydrogenase induced by an enantiomeric competitive inhibitor.
Authors: Nakashima, K. / Ito, K. / Nakajima, Y. / Yamazawa, R. / Miyakawa, S. / Yoshimoto, T.
History
DepositionOct 9, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)108,7689
Polymers106,7304
Non-polymers2,0395
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14900 Å2
ΔGint-113 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.115, 106.609, 164.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26682.389 Da / Num. of mol.: 4 / Mutation: T190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fragi (bacteria) / Plasmid: pkk233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue
References: UniProt: Q5KST5, 3-hydroxybutyrate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16%(w/v) PEG8000, 100mM magnesium chloride, 100mM HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 21, 2008 / Details: mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 86335 / Num. obs: 86335 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / Num. unique all: 7621 / % possible all: 88.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2ZTL

2ztl


Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4321 -random
Rwork0.238 ---
all-86158 --
obs-86158 98.3 %-
Displacement parametersBiso mean: 34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6601 0 134 633 7368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.693
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.305 371 -
Rwork0.286 --
obs-7337 84.8 %

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