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- PDB-3wtc: Crystal structure of Gox2036 -

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Basic information

Entry
Database: PDB / ID: 3wtc
TitleCrystal structure of Gox2036
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Dehydrogenase / reductase
Function / homology
Function and homology information


diacetyl reductase [(S)-acetoin forming] / diacetyl reductase ((S)-acetoin forming) activity / acetoin catabolic process
Similarity search - Function
Acetoin reductase / 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
Diacetyl reductase [(S)-acetoin forming]
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsYuan, Y.A. / Lin, J.P.
CitationJournal: To be Published
Title: Crystal structure of Gox0525
Authors: Yuan, Y.A. / Lin, J.P.
History
DepositionApr 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)54,7832
Polymers54,7832
Non-polymers00
Water6,612367
1
A: Putative oxidoreductase
B: Putative oxidoreductase

A: Putative oxidoreductase
B: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)109,5654
Polymers109,5654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13250 Å2
ΔGint-76 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.840, 58.098, 67.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21B-399-

HOH

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Components

#1: Protein Putative oxidoreductase /


Mass: 27391.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: 621H / Gene: GOX2036 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FPC4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG3350, HEPES, Proline, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 53326 / Num. obs: 53193 / % possible obs: 99.75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.65→1.69 Å / % possible all: 99.46

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V2G

3v2g


Resolution: 1.65→41.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.731 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17376 2847 5.1 %RANDOM
Rwork0.14776 ---
all0.148 ---
obs0.14907 53193 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.717 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å20 Å2
2--1.39 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 0 367 4163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193838
X-RAY DIFFRACTIONr_bond_other_d0.0020.023816
X-RAY DIFFRACTIONr_angle_refined_deg2.0711.9715188
X-RAY DIFFRACTIONr_angle_other_deg0.95738770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79325136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0231518
X-RAY DIFFRACTIONr_chiral_restr0.1320.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
LS refinement shellResolution: 1.652→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 214 -
Rwork0.17 3860 -
obs--99.46 %
Refinement TLS params.

T33: 0.0036 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
10.33320.2607-0.08530.2597-0.15870.2261-0.04070.03210.0243-0.00580.030.0126-0.0380.01030.01080.0182-0.0043-0.00640.01620.004768.439511.535724.8552
20.22140.03130.02330.16050.07830.25790.041-0.0362-0.00160.0018-0.0435-0.0198-0.01610.04280.00250.0219-0.0146-0.00320.03520.009373.25186.057354.9207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 259
2X-RAY DIFFRACTION2B1 - 259

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