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

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Basic information

Entry
Database: PDB / ID: 8yxq
TitleNADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of Imine Reductase wild type from Pochonia chlamydosporia 170
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / NADPH and 1-benzyl-4-methylpiperidin-3-onecomplex 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: 1.53 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 2, 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)64,15911
Polymers61,5092
Non-polymers2,6509
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13260 Å2
ΔGint-92 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.640, 114.800, 63.030
Angle α, β, γ (deg.)90.00, 99.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxidoreductase


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 (E. coli) / References: UniProt: A0A179FZ20

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Non-polymers , 5 types, 365 molecules

#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 203.280 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H17NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.68 %
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: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.52→57.43 Å / Num. obs: 456365 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.4
Reflection shellResolution: 1.52→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.274 / Num. unique obs: 27978

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→42.21 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.324 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21644 3906 5 %RANDOM
Rwork0.17648 ---
obs0.17849 74942 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.194 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å2-0 Å21.11 Å2
2---2.46 Å20 Å2
3----2.82 Å2
Refinement stepCycle: 1 / Resolution: 1.53→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 179 356 4779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134492
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174357
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6776108
X-RAY DIFFRACTIONr_angle_other_deg1.4531.61410133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16524.305151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62115766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0291514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
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_it2.5823.2142324
X-RAY DIFFRACTIONr_mcbond_other2.5823.2152325
X-RAY DIFFRACTIONr_mcangle_it3.474.8032892
X-RAY DIFFRACTIONr_mcangle_other3.4694.8042893
X-RAY DIFFRACTIONr_scbond_it3.973.7652168
X-RAY DIFFRACTIONr_scbond_other3.9693.7652169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.995.433217
X-RAY DIFFRACTIONr_long_range_B_refined7.19340.565018
X-RAY DIFFRACTIONr_long_range_B_other7.1740.244954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 286 -
Rwork0.343 5559 -
obs--99.08 %

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