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- PDB-2q2w: Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 2q2w
TitleStructure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
ComponentsBeta-D-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / Pseudomonas putida / D-3-Hydroxybutyrate Dehydrogenase
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
Beta-D-hydroxybutyrate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 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: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)106,0294
Polymers106,0294
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-87 kcal/mol
Surface area33970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.684, 58.814, 119.462
Angle α, β, γ (deg.)90.000, 93.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Beta-D-hydroxybutyrate dehydrogenase


Mass: 26507.275 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 20 % PEG1500, 0.2 mM 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: RIGAKU RUH3R / Wavelength: 1.5419 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.12→30 Å / Num. all: 1202 / Num. obs: 46410 / % possible obs: 99.1 % / Redundancy: 9.9 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.067 / Χ2: 0.867 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.12-2.27.60.36943681.217194.4
2.2-2.289.50.30345981.132198.9
2.28-2.39100.2445881.053199.1
2.39-2.5110.20.20646480.994199.3
2.51-2.6710.20.15846530.897199.6
2.67-2.8810.20.11746470.843199.8
2.88-3.1710.20.08546760.7691100
3.17-3.6210.30.05846980.6911100
3.62-4.5610.30.04247210.6451100
4.56-3010.10.03748130.587199.8

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Phasing

Phasing MRRfactor: 0.563 / Cor.coef. Fo:Fc: 0.379
Highest resolutionLowest resolution
Rotation3 Å29.8 Å
Translation3 Å29.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q2Q

2q2q


Resolution: 2.12→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.059 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2340 5.1 %RANDOM
Rwork0.181 ---
obs0.184 46306 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20.47 Å2
2--1.79 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 0 320 7712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0227537
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.94810278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58351000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.50624.639291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.487151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1921534
X-RAY DIFFRACTIONr_chiral_restr0.160.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025682
X-RAY DIFFRACTIONr_nbd_refined0.2160.23642
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.210
X-RAY DIFFRACTIONr_mcbond_it1.1061.55172
X-RAY DIFFRACTIONr_mcangle_it1.58727895
X-RAY DIFFRACTIONr_scbond_it2.93132783
X-RAY DIFFRACTIONr_scangle_it4.0484.52383
LS refinement shellResolution: 2.12→2.171 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 144 -
Rwork0.271 3070 -
obs-3214 93.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12950.38890.48280.981-0.231.4895-0.07150.03920.1083-0.26340.06170.1446-0.1771-0.13750.0098-0.0506-0.0043-0.0123-0.15920.0049-0.111716.7231.23511.42
21.19020.5346-0.40981.05420.07281.5542-0.014-0.0792-0.1429-0.12920.0104-0.242-0.06910.41370.0036-0.1166-0.02590.0428-0.0709-0.0058-0.061545.962-0.49319.326
31.33990.3097-0.01061.09270.14061.20470.0981-0.32520.03790.2201-0.11730.2462-0.0123-0.31080.0191-0.0813-0.02720.0520.0235-0.0126-0.09088.582-3.09641.075
41.38220.27810.21981.0565-0.21171.5180.1716-0.4374-0.0380.3215-0.1732-0.1299-0.18910.25230.0016-0.012-0.0966-0.02680.06820.0185-0.10937.5861.23249.372
54.898-3.9261.76625.0431-5.60599.29080.19820.35091.1372-0.73-0.32891.5353-1.2823-0.94430.13070.32590.1880.01880.14330.03430.3220.51425.81514.182
66.7192-3.2389-3.7628.7673.80692.9948-0.0729-0.28-0.27850.45410.1006-0.54950.50880.5091-0.02770.13120.0827-0.05860.0210.03580.024741.922-25.65918.327
75.89567.5082-3.152826.2641-7.67756.12670.16410.8408-0.9003-0.76180.26751.47290.8956-0.8857-0.43160.1931-0.0729-0.14340.1744-0.0230.304814.304-26.19440.557
83.50315.93380.447322.7451-5.55053.1920.3314-0.41820.75761.5654-0.674-0.3565-1.05880.09890.34260.3689-0.09880.03510.1681-0.12850.250531.76823.5148.084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1851 - 184
2X-RAY DIFFRACTION1AA213 - 256212 - 255
3X-RAY DIFFRACTION2BB2 - 1851 - 184
4X-RAY DIFFRACTION2BB213 - 256212 - 255
5X-RAY DIFFRACTION3CC2 - 1851 - 184
6X-RAY DIFFRACTION3CC213 - 256212 - 255
7X-RAY DIFFRACTION4DD2 - 1851 - 184
8X-RAY DIFFRACTION4DD213 - 256212 - 255
9X-RAY DIFFRACTION5AA186 - 212185 - 211
10X-RAY DIFFRACTION6BB186 - 212185 - 211
11X-RAY DIFFRACTION7CC186 - 212185 - 211
12X-RAY DIFFRACTION8DD186 - 212185 - 211

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