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- PDB-6kws: Crystal structure of Gre2 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 6kws
TitleCrystal structure of Gre2 from Candida albicans
ComponentsMethylglyoxal reductase (NADPH-dependent)
KeywordsOXIDOREDUCTASE / Gre2 / methylglyoxal reductase / NADPH
Function / homology3-beta hydroxysteroid dehydrogenase/isomerase family / : / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / Methylglyoxal reductase (NADPH-dependent)
Function and homology information
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNguyen, G.T. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2019R1A2C4069796 Korea, Republic Of
CitationJournal: Crystals / Year: 2019
Title: Crystal Structure of NADPH-Dependent Methylglyoxal Reductase Gre2 from Candida Albicans
Authors: Nguyen, G.T. / Kim, S. / Jin, H. / Cho, D.H. / Chun, H.S. / Kim, W.K. / Chang, J.H.
History
DepositionSep 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylglyoxal reductase (NADPH-dependent)


Theoretical massNumber of molelcules
Total (without water)37,4451
Polymers37,4451
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15540 Å2
Unit cell
Length a, b, c (Å)149.594, 149.594, 149.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Methylglyoxal reductase (NADPH-dependent)


Mass: 37445.188 Da / Num. of mol.: 1 / Mutation: Q52K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / Gene: orf19.5611, CAALFM_C603240WA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ABT9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.73 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate tribasic dihydrate (pH 5.6), 20%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13918 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.998 / Net I/σ(I): 43.8
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1384 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155: ???refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2108 593 -
Rwork0.1724 --
obs0.1762 13912 99.9 %
Refinement stepCycle: LAST / Resolution: 2.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 0 15 2626

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