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- PDB-2q2q: Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 2q2q
TitleStructure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
ComponentsBeta-D-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Pseudomonas putida / SDR
Function / homology
Function and homology information


3-hydroxybutyrate dehydrogenase / 3-hydroxybutyrate dehydrogenase activity / nucleotide binding
Similarity search - Function
3-hydroxybutyrate dehydrogenase / short chain dehydrogenase / PKS_KR / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Beta-D-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPaithankar, K.S. / Feller, C. / Kuettner, E.B. / Keim, A. / Grunow, M. / Strater, N.
CitationJournal: Febs J. / Year: 2007
Title: Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida.
Authors: Paithankar, K.S. / Feller, C. / Kuettner, E.B. / Keim, A. / Grunow, M. / Strater, N.
History
DepositionMay 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Beta-D-hydroxybutyrate dehydrogenase
B: Beta-D-hydroxybutyrate dehydrogenase
C: Beta-D-hydroxybutyrate dehydrogenase
D: Beta-D-hydroxybutyrate dehydrogenase
E: Beta-D-hydroxybutyrate dehydrogenase
F: Beta-D-hydroxybutyrate dehydrogenase
G: Beta-D-hydroxybutyrate dehydrogenase
H: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,03914
Polymers212,0588
Non-polymers3,9816
Water8,485471
1
A: Beta-D-hydroxybutyrate dehydrogenase
B: Beta-D-hydroxybutyrate dehydrogenase
C: Beta-D-hydroxybutyrate dehydrogenase
D: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3566
Polymers106,0294
Non-polymers1,3272
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-98 kcal/mol
Surface area32060 Å2
MethodPISA, PQS
2
E: Beta-D-hydroxybutyrate dehydrogenase
F: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules

E: Beta-D-hydroxybutyrate dehydrogenase
F: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6838
Polymers106,0294
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
MethodPQS
3
G: Beta-D-hydroxybutyrate dehydrogenase
H: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3414
Polymers53,0152
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Beta-D-hydroxybutyrate dehydrogenase
H: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules

G: Beta-D-hydroxybutyrate dehydrogenase
H: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6838
Polymers106,0294
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)261.457, 59.913, 116.523
Angle α, β, γ (deg.)90.000, 113.700, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-306-

HOH

21F-317-

HOH

31H-315-

HOH

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Components

#1: Protein
Beta-D-hydroxybutyrate dehydrogenase


Mass: 26507.275 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: bdhA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AE70, 3-hydroxybutyrate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal growTemperature: 295 K / pH: 7.1
Details: 17-20 % PEG 1500, 0.2mM calcium chloride, 10mM acetoacetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5419 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.02→30 Å / Num. obs: 105219 / % possible obs: 96.7 %
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.593 / % possible all: 74.4

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Phasing

Phasing MRRfactor: 0.572 / Cor.coef. Fo:Fc: 0.297
Highest resolutionLowest resolution
Rotation3 Å29.95 Å
Translation3 Å29.95 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMB

1wmb


Resolution: 2.02→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.117 / SU ML: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.274 5241 5 %
Rwork0.199 --
obs0.202 104909 96.4 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 42.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å2-1.37 Å2
2--3.16 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.02→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14526 0 264 471 15261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02215100
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.96920635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68451963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3924.442565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.869152261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0991569
X-RAY DIFFRACTIONr_chiral_restr0.1680.22440
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211255
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.27433
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.210067
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2676
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.161.510107
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.683215509
X-RAY DIFFRACTIONr_scbond_it3.04135833
X-RAY DIFFRACTIONr_scangle_it4.1864.55126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.07 Å
RfactorNum. reflection% reflection
Rfree0.372 273 -
Rwork0.259 5444 -
obs--71.15 %

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