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- PDB-8ozv: Imine Reductase from Ajellomyces dermatitidis in complex with 2,2... -

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Basic information

Entry
Database: PDB / ID: 8ozv
TitleImine Reductase from Ajellomyces dermatitidis in complex with 2,2-difluoroacetophenone
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Imine reductase / Amine / Dehydrogenase / NADP
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / 2,2-bis(fluoranyl)-1-phenyl-ethanone / Oxidoreductase
Similarity search - Component
Biological speciesBlastomyces dermatitidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0303
Polymers30,1291
Non-polymers9022
Water7,620423
1
A: Oxidoreductase
hetero molecules

A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0606
Polymers60,2572
Non-polymers1,8034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area11610 Å2
ΔGint-97 kcal/mol
Surface area19480 Å2
Unit cell
Length a, b, c (Å)74.000, 74.000, 112.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

21A-533-

HOH

31A-812-

HOH

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Components

#1: Protein Oxidoreductase


Mass: 30128.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastomyces dermatitidis (fungus) / Gene: BDBG_03427 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179UH34
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-W65 / 2,2-bis(fluoranyl)-1-phenyl-ethanone


Mass: 156.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6F2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 100 mM PO4 buffer pH 8.6; 0.2 M MgCl2; 20% (w/v) PEG 3350; 2M NADP+; 10 mM ligand

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.52→42.22 Å / Num. obs: 55313 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.014 / Net I/σ(I): 52.1
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 24 / Num. unique obs: 2742 / CC1/2: 1 / Rpim(I) all: 0.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→42.22 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.735 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14714 2799 5.1 %RANDOM
Rwork0.13153 ---
obs0.13233 52466 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.12 Å20 Å2
2--0.23 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.52→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 59 431 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122247
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162142
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.643085
X-RAY DIFFRACTIONr_angle_other_deg0.6331.5644937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.831511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47210347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3651.2191164
X-RAY DIFFRACTIONr_mcbond_other1.3661.2181164
X-RAY DIFFRACTIONr_mcangle_it2.0292.1811457
X-RAY DIFFRACTIONr_mcangle_other2.0342.1831458
X-RAY DIFFRACTIONr_scbond_it2.6861.4681083
X-RAY DIFFRACTIONr_scbond_other2.6851.471084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8662.5781620
X-RAY DIFFRACTIONr_long_range_B_refined5.69318.882780
X-RAY DIFFRACTIONr_long_range_B_other5.19614.062594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 213 -
Rwork0.133 3829 -
obs--99.95 %

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