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- PDB-2q2v: Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 2q2v
TitleStructure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas putida
ComponentsBeta-D-hydroxybutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / D-3-Hydroxybutyrate Dehydrogenase / 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: 1.9 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 ...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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0197
Polymers106,0294
Non-polymers1,9903
Water8,053447
1
A: Beta-D-hydroxybutyrate dehydrogenase
B: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules

A: Beta-D-hydroxybutyrate dehydrogenase
B: 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
crystal symmetry operation2_655-x+1,y,-z1
Buried area13740 Å2
ΔGint-101 kcal/mol
Surface area32630 Å2
MethodPISA, PQS
2
C: Beta-D-hydroxybutyrate dehydrogenase
D: 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
Buried area16020 Å2
ΔGint-113 kcal/mol
Surface area30420 Å2
MethodPISA
3
B: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules

A: Beta-D-hydroxybutyrate dehydrogenase

D: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules

C: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0197
Polymers106,0294
Non-polymers1,9903
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area10510 Å2
ΔGint-74 kcal/mol
Surface area35890 Å2
MethodPISA
4
C: Beta-D-hydroxybutyrate dehydrogenase
D: Beta-D-hydroxybutyrate dehydrogenase
hetero molecules

C: Beta-D-hydroxybutyrate dehydrogenase
D: 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_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)115.328, 58.176, 119.382
Angle α, β, γ (deg.)90.000, 92.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-257-

HOH

21B-304-

HOH

31C-333-

HOH

41D-301-

HOH

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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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 447 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / 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: 1.9→30 Å / Num. obs: 62236 / % possible obs: 99.5 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.048 / Χ2: 0.931 / Net I/σ(I): 20.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11 % / Rmerge(I) obs: 0.154 / Num. unique all: 6088 / Χ2: 1.007 / % possible all: 98.3

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Phasing

Phasing MRRfactor: 0.584 / Cor.coef. Fo:Fc: 0.254
Highest resolutionLowest resolution
Rotation3 Å29.82 Å
Translation3 Å29.82 Å

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Processing

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

2q2q


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.151 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3157 5.1 %RANDOM
Rwork0.169 ---
obs0.171 62171 99.33 %-
all-1443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.45 Å2
2--0.68 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7374 0 132 447 7953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227661
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.96910467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30724.502291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.638151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5961536
X-RAY DIFFRACTIONr_chiral_restr0.1360.21235
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025723
X-RAY DIFFRACTIONr_nbd_refined0.2120.23721
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2409
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.2201
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.257
X-RAY DIFFRACTIONr_mcbond_it0.7651.55076
X-RAY DIFFRACTIONr_mcangle_it1.20727864
X-RAY DIFFRACTIONr_scbond_it2.22832943
X-RAY DIFFRACTIONr_scangle_it3.284.52603
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 243 -
Rwork0.17 4274 -
obs-4517 98.24 %
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)
10.9314-0.00640.20850.4149-0.20820.51910.03750.0729-0.0685-0.042-0.02130.12820.0613-0.1041-0.0162-0.1037-0.00320.0046-0.102-0.0141-0.088339.4714-1.4849-11.8722
21.01550.0602-0.05770.6468-0.15510.62770.0176-0.22980.02830.09290.00770.0825-0.0261-0.113-0.0254-0.1246-0.00190.0113-0.0719-0.007-0.105345.42661.779417.8667
30.86380.1340.07421.5980.2311.25990.0417-0.0758-0.09320.1277-0.0358-0.37830.00430.301-0.0059-0.0207-0.0082-0.0429-0.00930.0251-0.007716.91221.058669.354
40.7403-0.0215-0.11560.62230.06141.40920.05160.12710.0202-0.1503-0.0605-0.1463-0.04580.17630.0089-0.00770.02630.02-0.03360.0182-0.05367.70294.224440.4881
51.47451.24021.11976.03551.59470.93560.06870.1084-0.4264-0.1957-0.058-0.05070.36710.1541-0.01060.07320.010.02220.0224-0.01310.053340.4706-25.9559-7.3855
62.78890.9643-0.42854.1076-1.49895.4704-0.0106-0.00760.55990.4414-0.129-0.299-0.5820.23680.13960.00090.0218-0.0096-0.0703-0.00260.106749.898424.553413.6938
74.9096-0.80281.862511.7276-6.87497.571-0.2158-0.2903-1.29790.15690.3989-0.26120.849-0.6923-0.18310.27220.06410.10510.16030.03540.230610.7817-20.385867.557
82.0519-4.6604-1.08515.5524-4.773412.5408-0.39370.18950.5269-0.53880.06660.5047-0.9570.05440.32710.2554-0.0566-0.09170.19630.07360.21423.802225.462545.4719
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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