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- PDB-8y12: NADPH complex of Imine Reductase from Pochonia chlamydosporia 170 -

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Basic information

Entry
Database: PDB / ID: 8y12
TitleNADPH complex of Imine Reductase from Pochonia chlamydosporia 170
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / NADPH Complex / Reductive aminase
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / Oxidoreductase
Similarity search - Component
Biological speciesPochonia chlamydosporia 170 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShi, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: NADPH complex of Imine Reductase from Pochonia chlamydosporia 170
Authors: Shi, M.
History
DepositionJan 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2086
Polymers61,5092
Non-polymers1,6994
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-86 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.802, 114.091, 62.870
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oxidoreductase / Imine reductase


Mass: 30754.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pochonia chlamydosporia 170 (fungus) / Gene: VFPPC_03305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179FZ20
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, magnesium chloride, Tris-Hcl 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jul 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.09→33.08 Å / Num. obs: 30773 / % possible obs: 99.1 % / Redundancy: 5.29 % / CC1/2: 0.0538 / Net I/σ(I): 17.53
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.1537 / Mean I/σ(I) obs: 4.33 / Num. unique obs: 1428 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.715 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25489 1540 5.1 %RANDOM
Rwork0.18128 ---
obs0.18502 28926 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.787 Å2
Baniso -1Baniso -2Baniso -3
1-4.54 Å2-0 Å20.65 Å2
2---1.85 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 2.1→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4221 0 110 336 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134397
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174254
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.6595980
X-RAY DIFFRACTIONr_angle_other_deg1.2971.5829892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84724.267150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29615760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5251514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
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_it2.0883.1242298
X-RAY DIFFRACTIONr_mcbond_other2.0883.1242297
X-RAY DIFFRACTIONr_mcangle_it3.1164.6822869
X-RAY DIFFRACTIONr_mcangle_other3.1154.6822870
X-RAY DIFFRACTIONr_scbond_it2.5543.4372099
X-RAY DIFFRACTIONr_scbond_other2.5543.4372100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9535.0113112
X-RAY DIFFRACTIONr_long_range_B_refined5.4638.8265078
X-RAY DIFFRACTIONr_long_range_B_other5.45538.7115031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 105 -
Rwork0.247 2050 -
obs--97.6 %

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