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- PDB-7wbc: Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4... -

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Basic information

Entry
Database: PDB / ID: 7wbc
TitleHydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4S)-2-2-methyl-2,4-pentanediol
ComponentsSDR family NAD(P)-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Hydroxysteroid dehydrogenase / Complex / NAD+
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / :
Function and homology information
Biological speciesRhodococcus ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShi, S.-C. / Zheng, Y.-C. / Xu, J.-H. / Li, C.-X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4S)-2-2-methyl-2,4-pentanediol
Authors: Shi, S.-C. / Zheng, Y.-C. / Xu, J.-H. / Li, C.-X.
History
DepositionDec 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 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
A: SDR family NAD(P)-dependent oxidoreductase
B: SDR family NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,84913
Polymers54,8622
Non-polymers1,98711
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-80 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.989, 110.270, 125.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-574-

HOH

21B-539-

HOH

31B-540-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SDR family NAD(P)-dependent oxidoreductase / SDR family oxidoreductase


Mass: 27430.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus ruber (bacteria) / Gene: DCN13_20495, F1734_22905 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U2VFT3

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Non-polymers , 6 types, 346 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2-(N-Morpholino) ethane sulfonic acid, MgCl2, CaCl2, MPD, P3350, 2-(N-morpholino) ethane sulfonic acid, imidazole

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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: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→33.3 Å / Num. obs: 30411 / % possible obs: 95.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.979 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1560 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JY1

5jy1


Resolution: 2→33.3 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1596 5.33 %
Rwork0.176 28355 -
obs0.1788 29951 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.82 Å2 / Biso mean: 26.0029 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: final / Resolution: 2→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3710 0 127 335 4172
Biso mean--29.25 31.57 -
Num. residues----500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.060.27481110.247225083
2.07-2.140.35441400.2627256094
2.14-2.220.24461470.18082700100
2.22-2.330.3148980.2335193171
2.33-2.450.23061340.17082710100
2.45-2.60.23431690.17792688100
2.6-2.80.24781730.1919264397
2.8-3.080.22961370.17752732100
3.08-3.530.24651490.1791266297
3.53-4.440.1861560.151263295
4.45-50.1911820.14842847100

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