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- PDB-5b4u: Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcal... -

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Basic information

Entry
Database: PDB / ID: 5b4u
TitleCrystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor malonate
Components3-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Short-chain dehydrogenases/reductases / inhibitor / complex / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
MALONIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsKanazawa, H. / Tsunoda, M. / Hoque, M.M. / Suzuki, K. / Yamamoto, T. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase
Authors: Kanazawa, H. / Hoque, M.M. / Tsunoda, M. / Suzuki, K. / Yamamoto, T. / Kawai, G. / Kondo, J. / Takenaka, A.
History
DepositionApr 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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
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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9455
Polymers27,1191
Non-polymers8264
Water5,945330
1
A: 3-hydroxybutyrate dehydrogenase
hetero molecules

A: 3-hydroxybutyrate dehydrogenase
hetero molecules

A: 3-hydroxybutyrate dehydrogenase
hetero molecules

A: 3-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,77920
Polymers108,4764
Non-polymers3,30416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area18420 Å2
ΔGint-221 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.830, 62.830, 119.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-303-

NA

21A-722-

HOH

31A-730-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-hydroxybutyrate dehydrogenase / D-3-hydroxybutyrate dehydrogenase


Mass: 27118.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: UZ73_03715 / Production host: Escherichia coli (E. coli)
References: UniProt: D0VWQ0, 3-hydroxybutyrate dehydrogenase

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Non-polymers , 5 types, 334 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG 4000, 100mM Tris hydrochloride pH 8.5, 200mM malonate, 5mM NAD+, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→23 Å / Num. obs: 42260 / % possible obs: 98 % / Redundancy: 13.5 % / Rsym value: 0.118 / Net I/av σ(I): 5.045 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.45-1.5313.40.2622.61100
1.53-1.6213.70.2033.41100
1.62-1.7313.80.174.11100
1.73-1.8713.90.1424.81100
1.87-2.05140.1195.51100
2.05-2.29140.1016.41100
2.29-2.6513.80.0926.91100
2.65-3.2413.30.097.1199.1
3.24-4.5910.80.0937.1184.2
4.59-239.30.0976.7168.3

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementResolution: 1.45→20.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.713 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1511 4182 9.9 %RANDOM
Rwork0.1344 ---
obs0.1361 37972 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.57 Å2 / Biso mean: 9.104 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.45→20.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 53 330 2289
Biso mean--5.49 22.01 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0192025
X-RAY DIFFRACTIONr_bond_other_d00.021975
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.9892767
X-RAY DIFFRACTIONr_angle_other_deg0.52934550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56925.55672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66815332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.445157
X-RAY DIFFRACTIONr_chiral_restr0.0550.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022314
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02430
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 321 -
Rwork0.141 2812 -
all-3133 -
obs--99.84 %

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