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- PDB-5gmo: X-ray structure of carbonyl reductase SsCR -

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Basic information

Entry
Database: PDB / ID: 5gmo
TitleX-ray structure of carbonyl reductase SsCR
ComponentsProtein induced by osmotic stress
KeywordsOXIDOREDUCTASE / carbonyl reductase
Function / homology
Function and homology information


cinnamyl-alcohol dehydrogenase / cinnamyl-alcohol dehydrogenase activity / nucleotide binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein induced by osmotic stress
Similarity search - Component
Biological speciesScheffersomyces stipitis CBS 6054 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsShang, Y.P. / Yu, H.L. / Xu, J.H.
Funding support China, 3items
OrganizationGrant numberCountry
the National Natural Science Foundation of China21276082 China
Shanghai Science and Technology Program15JC1400403 China
SKLBE2060204 China
CitationJournal: Adv.Synth.Catal. / Year: 2017
Title: Efficient Synthesis of (R)-2-Chloro-1-(2,4-dichlorophenyl)ethanol with a Ketoreductase from Scheffersomyces stipitis CBS 6045
Authors: Shang, Y.P. / Chen, Q. / Kong, X.D. / Zhang, Y.J. / Xu, J.H. / Yu, H.L.
History
DepositionJul 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Nov 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
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: Protein induced by osmotic stress


Theoretical massNumber of molelcules
Total (without water)37,0061
Polymers37,0061
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.648, 52.862, 140.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein induced by osmotic stress / carbonyl reductase SsCR


Mass: 37005.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus)
Strain: CBS 6054 / Gene: GRP3.1, PICST_32463
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: A3LWG4, cinnamyl-alcohol dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride, 30%(w/v) Polyethylene glycol 4000
PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 16249 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PVD

4pvd


Resolution: 2.304→39.401 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.06
RfactorNum. reflection% reflection
Rfree0.2379 815 5.04 %
Rwork0.1819 --
obs0.1848 16167 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.304→39.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 0 243 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072643
X-RAY DIFFRACTIONf_angle_d1.0343579
X-RAY DIFFRACTIONf_dihedral_angle_d14.898970
X-RAY DIFFRACTIONf_chiral_restr0.071411
X-RAY DIFFRACTIONf_plane_restr0.005457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3041-2.44850.25081180.20082431X-RAY DIFFRACTION97
2.4485-2.63750.32131340.20962561X-RAY DIFFRACTION100
2.6375-2.90280.2981470.20132506X-RAY DIFFRACTION100
2.9028-3.32270.2611330.19392570X-RAY DIFFRACTION100
3.3227-4.18550.21131470.16282575X-RAY DIFFRACTION100
4.1855-4.950.19541360.17052709X-RAY DIFFRACTION99

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