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- PDB-8p2j: Imine Reductase from Ajellomyces dermatitidis in space group C21 -

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Basic information

Entry
Database: PDB / ID: 8p2j
TitleImine Reductase from Ajellomyces dermatitidis in space group C21
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 / Oxidoreductase
Similarity search - Component
Biological speciesBlastomyces dermatitidis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
C: Oxidoreductase
D: Oxidoreductase
E: Oxidoreductase
F: Oxidoreductase
G: Oxidoreductase
H: Oxidoreductase
I: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,38918
Polymers276,6809
Non-polymers6,7099
Water35,1831953
1
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers61,4852
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-83 kcal/mol
Surface area21530 Å2
MethodPISA
2
C: Oxidoreductase
D: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers61,4852
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-92 kcal/mol
Surface area21020 Å2
MethodPISA
3
E: Oxidoreductase
F: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers61,4852
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-88 kcal/mol
Surface area21130 Å2
MethodPISA
4
G: Oxidoreductase
H: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers61,4852
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-91 kcal/mol
Surface area21010 Å2
MethodPISA
5
I: Oxidoreductase
hetero molecules

I: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9754
Polymers61,4852
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10250 Å2
ΔGint-79 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.620, 87.970, 162.580
Angle α, β, γ (deg.)90.00, 108.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11I-487-

HOH

21I-633-

HOH

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Components

#1: Protein
Oxidoreductase


Mass: 30742.277 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastomyces dermatitidis (fungus) / Gene: BDBG_03427 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A179UH34
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1953 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0; 0.2 M MgCl2; 20% PEG 6000

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 1.73→97.16 Å / Num. obs: 278614 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 1.73→1.77 Å / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 20244 / CC1/2: 0.51 / Rpim(I) all: 0.71

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→97.16 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.338 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19326 13858 5 %RANDOM
Rwork0.16634 ---
obs0.16767 264735 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.594 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.12 Å2
2--0.33 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.73→97.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18882 0 432 1961 21275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01219784
X-RAY DIFFRACTIONr_bond_other_d0.0010.01618797
X-RAY DIFFRACTIONr_angle_refined_deg1.51.63827059
X-RAY DIFFRACTIONr_angle_other_deg0.5061.56143210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41752607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.829589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.705102949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.23238
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024123
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_it2.5392.65910404
X-RAY DIFFRACTIONr_mcbond_other2.5392.65910404
X-RAY DIFFRACTIONr_mcangle_it3.4464.77112992
X-RAY DIFFRACTIONr_mcangle_other3.4464.77112993
X-RAY DIFFRACTIONr_scbond_it4.1753.1019380
X-RAY DIFFRACTIONr_scbond_other4.1753.1019378
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2325.514059
X-RAY DIFFRACTIONr_long_range_B_refined7.04528.9422640
X-RAY DIFFRACTIONr_long_range_B_other6.99827.4122198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 1042 -
Rwork0.286 19200 -
obs--96.51 %

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