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- PDB-8yxy: NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of I... -

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Entry
Database: PDB / ID: 8yxy
TitleNADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of Imine Reductase Mutant(M6) from Pochonia chlamydosporia 170
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure / Imine reductase
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsShi, M. / Zheng, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of Imine Reductase wild type from Pochonia chlamydosporia 170
Authors: Shi, M. / Zheng, G.
History
DepositionApr 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 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)63,2148
Polymers61,1082
Non-polymers2,1066
Water12,683704
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-91 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.850, 114.450, 62.610
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oxidoreductase / Imine reductase


Mass: 30554.055 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 (E. coli) / References: UniProt: A0A179FZ20
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-A1D7O / (4~{R})-4-methyl-1-(phenylmethyl)piperidin-3-one


Mass: 203.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG3350, magnesium chloride, Tris-Hcl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.13→42.03 Å / Num. obs: 865651 / % possible obs: 78.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 7.9
Reflection shellResolution: 1.13→1.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.297 / Num. unique obs: 149418

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→42.03 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.534 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17557 7541 5 %RANDOM
Rwork0.1539 ---
obs0.15501 141826 78.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.347 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20.2 Å2
2---0.51 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.13→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 140 704 5050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134406
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174247
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.6715995
X-RAY DIFFRACTIONr_angle_other_deg1.6181.5979884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88324.771153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54515751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6091514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
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_it1.2641.3242312
X-RAY DIFFRACTIONr_mcbond_other1.2641.3262313
X-RAY DIFFRACTIONr_mcangle_it1.7621.9862883
X-RAY DIFFRACTIONr_mcangle_other1.7621.9882884
X-RAY DIFFRACTIONr_scbond_it2.7851.6932094
X-RAY DIFFRACTIONr_scbond_other2.7851.6952095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0982.4033113
X-RAY DIFFRACTIONr_long_range_B_refined5.23418.8735172
X-RAY DIFFRACTIONr_long_range_B_other5.05917.9354980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 92 -
Rwork0.287 1495 -
obs--11.21 %

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