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- PDB-8yvh: NADPH complex of Imine Reductase Mutant(M6) from Pochonia chlamyd... -

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Basic information

Entry
Database: PDB / ID: 8yvh
TitleNADPH complex of Imine Reductase Mutant(M6) from Pochonia chlamydosporia 170
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / NADPH complex of Mutant(M6) / 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 / Oxidoreductase
Similarity search - Component
Biological speciesPochonia chlamydosporia 170 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShi, M. / zheng, G.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: NADPH complex of Imine Reductase Mutant(M6) from Pochonia chlamydosporia 170
Authors: Shi, M.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 2.0Apr 16, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2665
Polymers65,6572
Non-polymers1,6093
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-86 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.398, 117.950, 63.529
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oxidoreductase


Mass: 32828.449 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-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
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: 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→35.09 Å / Num. obs: 36140 / % possible obs: 98.4 % / Redundancy: 3.99 % / Rmerge(I) obs: 0.0638 / Net I/σ(I): 13.36
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.08 % / Rmerge(I) obs: 0.1661 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 1528 / % possible all: 84.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.09 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.368 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 1596 5.1 %RANDOM
Rwork0.16687 ---
obs0.17061 29740 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: 22.384 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å2-0.41 Å2
2--0.33 Å2-0 Å2
3----1.59 Å2
Refinement stepCycle: 1 / Resolution: 2.1→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 104 455 4782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134386
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174211
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6615974
X-RAY DIFFRACTIONr_angle_other_deg1.3271.5829799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84524.771153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55615753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9431514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
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_it1.5252.2322319
X-RAY DIFFRACTIONr_mcbond_other1.5262.2322318
X-RAY DIFFRACTIONr_mcangle_it2.3063.3422894
X-RAY DIFFRACTIONr_mcangle_other2.3053.3422895
X-RAY DIFFRACTIONr_scbond_it2.1922.5052067
X-RAY DIFFRACTIONr_scbond_other2.1922.5052068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3263.6453081
X-RAY DIFFRACTIONr_long_range_B_refined5.08428.6775077
X-RAY DIFFRACTIONr_long_range_B_other5.00928.4224987
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
Rfree0.284 119 -
Rwork0.209 2191 -
obs--99.44 %

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