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- PDB-7e6o: Crystal structure of polyol dehydrogenase from Paracoccus denitri... -

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Basic information

Entry
Database: PDB / ID: 7e6o
TitleCrystal structure of polyol dehydrogenase from Paracoccus denitrificans
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase / sorbitol oxidation
Function / homologyshort chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSha, F. / Zheng, Y.C.
CitationJournal: To Be Published
Title: Crystal structure of polyol dehydrogenase from Paracoccus denitrificans
Authors: Sha, F. / Zheng, Y.C. / Gao, J.
History
DepositionFeb 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Short-chain dehydrogenase/reductase SDR
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)111,1244
Polymers111,1244
Non-polymers00
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-85 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.710, 86.892, 134.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR


Mass: 27780.877 Da / Num. of mol.: 4 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_4841 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1BBK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5 / Details: 0.1 M MES, pH 6.5 15% (w/v) PEG 6000 5% (w/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 686828 / % possible obs: 99.4 % / Redundancy: 12.8 % / CC1/2: 0.991 / Net I/σ(I): 20.37
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2623 / CC1/2: 0.775 / CC star: 0.934 / Χ2: 0.939

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K2W

1k2w


Resolution: 2.1→43.97 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.611 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2523 5 %RANDOM
Rwork0.1601 ---
obs0.1624 48148 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.03 Å2 / Biso mean: 28.542 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3---0.76 Å2
Refinement stepCycle: final / Resolution: 2.1→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7170 0 0 503 7673
Biso mean---36.12 -
Num. residues----987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137251
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177007
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6399796
X-RAY DIFFRACTIONr_angle_other_deg1.371.60216084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21520.455286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.465151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7911549
X-RAY DIFFRACTIONr_chiral_restr0.0750.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021533
LS refinement shellResolution: 2.104→2.159 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 157 -
Rwork0.184 2603 -
all-2760 -
obs--70.37 %

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