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- PDB-8k1i: Crystal structure of arabinose dehydrogenase from Candida auris -

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Basic information

Entry
Database: PDB / ID: 8k1i
TitleCrystal structure of arabinose dehydrogenase from Candida auris
ComponentsNADP-dependent oxidoreductase domain-containing protein
KeywordsOXIDOREDUCTASE
Function / homologyoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / NADP-dependent oxidoreductase domain-containing protein
Function and homology information
Biological species[Candida] auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsZhang, J. / Bai, X. / He, S.R. / Zhao, Z.D.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of arabinose dehydrogenase from Candida auris
Authors: Zhang, J. / Bai, X. / He, S.R. / Zhao, Z.D.
History
DepositionJul 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent oxidoreductase domain-containing protein
B: NADP-dependent oxidoreductase domain-containing protein
C: NADP-dependent oxidoreductase domain-containing protein
D: NADP-dependent oxidoreductase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)159,3544
Polymers159,3544
Non-polymers00
Water7,656425
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.634, 91.119, 227.712
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
NADP-dependent oxidoreductase domain-containing protein / arabinose dehydrogenase


Mass: 39838.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Candida] auris (fungus) / Gene: QG37_02322 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L0P3H9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Tris-HCL, magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→34.3 Å / Num. obs: 109522 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.9983 / Rmerge(I) obs: 0.1208 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2 Å / Rpim(I) all: 0.035

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→30.64 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 33.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3137 5508 5.03 %
Rwork0.2549 --
obs0.2578 109522 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11086 0 0 425 11511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911335
X-RAY DIFFRACTIONf_angle_d1.0715354
X-RAY DIFFRACTIONf_dihedral_angle_d5.9081511
X-RAY DIFFRACTIONf_chiral_restr0.0571712
X-RAY DIFFRACTIONf_plane_restr0.011954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.36191930.33463371X-RAY DIFFRACTION99
1.97-1.990.34041960.31853444X-RAY DIFFRACTION100
1.99-2.020.34692140.31553359X-RAY DIFFRACTION100
2.02-2.040.37442050.31373446X-RAY DIFFRACTION100
2.04-2.070.38341660.31733417X-RAY DIFFRACTION100
2.07-2.10.39221940.32013396X-RAY DIFFRACTION100
2.1-2.130.35972100.31063407X-RAY DIFFRACTION100
2.13-2.160.32941810.30133412X-RAY DIFFRACTION100
2.16-2.20.34032010.30453398X-RAY DIFFRACTION100
2.2-2.230.40181670.30513474X-RAY DIFFRACTION100
2.23-2.270.37391760.3063434X-RAY DIFFRACTION100
2.27-2.310.37481830.29673448X-RAY DIFFRACTION100
2.31-2.360.35231660.29663417X-RAY DIFFRACTION100
2.36-2.40.37521620.29813486X-RAY DIFFRACTION100
2.4-2.460.3291720.28863444X-RAY DIFFRACTION100
2.46-2.510.35431810.29813436X-RAY DIFFRACTION100
2.51-2.580.39982050.30573432X-RAY DIFFRACTION100
2.58-2.650.35931540.29543474X-RAY DIFFRACTION100
2.65-2.720.34951830.29293436X-RAY DIFFRACTION100
2.72-2.810.35491720.29083487X-RAY DIFFRACTION100
2.81-2.910.35522130.28853431X-RAY DIFFRACTION100
2.91-3.030.30011630.28343495X-RAY DIFFRACTION100
3.03-3.170.35341850.29223457X-RAY DIFFRACTION100
3.17-3.330.33511670.27683507X-RAY DIFFRACTION100
3.33-3.540.31471580.25583514X-RAY DIFFRACTION100
3.54-3.810.27782010.23873500X-RAY DIFFRACTION100
3.81-4.20.281830.2163510X-RAY DIFFRACTION100
4.2-4.80.25551890.19773551X-RAY DIFFRACTION100
4.8-6.040.29061850.21413575X-RAY DIFFRACTION100
6.04-30.640.24441830.18753747X-RAY DIFFRACTION100

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