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- PDB-8ozw: Imine Reductase from Ajellomyces dermatitidis in complex NADPH4 -

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Basic information

Entry
Database: PDB / ID: 8ozw
TitleImine Reductase from Ajellomyces dermatitidis in complex NADPH4
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Imine reductase / Amine / Dehydrogenase / NADP
Function / homology3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NADP binding / oxidoreductase activity / NAD(P)-binding domain superfamily / Chem-TXP / Oxidoreductase
Function and homology information
Biological speciesBlastomyces dermatitidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsSharma, M. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M006832/1 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structure of the imine reductase from Ajellomyces dermatitidis in three crystal forms.
Authors: Sharma, M. / Cuetos, A. / Willliams, A. / Gonzalez-Martinez, D. / Grogan, G.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0674
Polymers60,2572
Non-polymers8102
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-89 kcal/mol
Surface area20980 Å2
Unit cell
Length a, b, c (Å)89.390, 89.390, 136.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Oxidoreductase


Mass: 30128.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastomyces dermatitidis (fungus) / Gene: BDCG_07742 / Production host: Escherichia coli (E. coli) / References: UniProt: C5GTJ9
#2: Chemical ChemComp-TXP / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE


Mass: 747.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H32N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M PCTP pH 4.0; 25% (w/v) PEG 1500; protein at 10 mg per mL with 2 mM NADPH4

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.01→77.41 Å / Num. obs: 42264 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.05 / Net I/σ(I): 19.9
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3099 / CC1/2: 0.64 / Rpim(I) all: 0.66

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→77.41 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.2 --
obs-42264 98.8 %
Refinement stepCycle: LAST / Resolution: 2.01→77.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 52 366 4550

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