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- PDB-5b6k: Crystal structure of Ketoreductase 1 from Candida glabrata -

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Basic information

Entry
Database: PDB / ID: 5b6k
TitleCrystal structure of Ketoreductase 1 from Candida glabrata
ComponentsUncharacterized protein CgKR1
KeywordsOXIDOREDUCTASE / ketoreductase
Function / homology
Function and homology information


fungal biofilm matrix / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / cytosol
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
Candida glabrata strain CBS138 chromosome E complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.701 Å
AuthorsQin, B. / Mori, T. / Abe, I. / You, S.
CitationJournal: To Be Published
Title: Engineering of Candida glabrata Ketoreductase 1 for Asymmetric Reduction of alpha-Halo Ketones
Authors: Qin, F. / Qin, B. / Mori, T. / Wang, Y. / Meng, L. / Zhang, X. / Jia, X. / Abe, I. / You, S.
History
DepositionMay 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein CgKR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8522
Polymers40,7561
Non-polymers961
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.620, 61.620, 189.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Uncharacterized protein CgKR1


Mass: 40755.969 Da / Num. of mol.: 1 / Fragment: UNP residues 8-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (fungus)
Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
Gene: GRE2(A), CAGL0E05170g / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q6FV31
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100mM sodium citrate buffer (pH 5.5), 1995mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 44487 / % possible obs: 99.7 % / Redundancy: 7.58 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.32
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.37 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 5.23 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.701→35.473 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.34
RfactorNum. reflection% reflection
Rfree0.1905 2225 5 %
Rwork0.1678 --
obs0.169 44485 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.701→35.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 5 352 3000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072701
X-RAY DIFFRACTIONf_angle_d0.8393654
X-RAY DIFFRACTIONf_dihedral_angle_d15.735987
X-RAY DIFFRACTIONf_chiral_restr0.056415
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.73750.24371390.22332627X-RAY DIFFRACTION100
1.7375-1.7780.25811380.20842634X-RAY DIFFRACTION100
1.778-1.82240.24971390.19352642X-RAY DIFFRACTION100
1.8224-1.87170.21951410.182668X-RAY DIFFRACTION100
1.8717-1.92680.17921380.17442634X-RAY DIFFRACTION100
1.9268-1.9890.22171410.18192671X-RAY DIFFRACTION100
1.989-2.060.22561380.17782629X-RAY DIFFRACTION100
2.06-2.14250.1761390.17572635X-RAY DIFFRACTION100
2.1425-2.240.19121380.16742628X-RAY DIFFRACTION100
2.24-2.35810.1981410.16862677X-RAY DIFFRACTION100
2.3581-2.50580.21621380.17022618X-RAY DIFFRACTION100
2.5058-2.69920.18221400.17712652X-RAY DIFFRACTION100
2.6992-2.97070.17011390.17882643X-RAY DIFFRACTION100
2.9707-3.40030.19851400.16282659X-RAY DIFFRACTION100
3.4003-4.28280.15621380.14242630X-RAY DIFFRACTION99
4.2828-35.48090.18591380.15822613X-RAY DIFFRACTION98

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