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- PDB-8hwy: Ancestral imine reductase mutant N559_M6 -

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Basic information

Entry
Database: PDB / ID: 8hwy
TitleAncestral imine reductase mutant N559_M6
Componentsancestral imine reductase mutant N559_M6
KeywordsOXIDOREDUCTASE / ancestral enzyme / NADP+
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesEscherichia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZhu, X.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21878085 China
CitationJournal: To Be Published
Title: The evolution of stereoselectivity in imine reductase
Authors: Zhu, X.X. / Zheng, G.W.
History
DepositionJan 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ancestral imine reductase mutant N559_M6
B: ancestral imine reductase mutant N559_M6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2244
Polymers61,7382
Non-polymers1,4872
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-92 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.336, 71.762, 65.108
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ancestral imine reductase mutant N559_M6


Mass: 30868.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for this entry is not available in UniProt at the time of biocuration.
Source: (gene. exp.) Escherichia (bacteria) / Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1M Bis-Tris (pH = 6.5), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2022
RadiationMonochromator: Si11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.32→59.84 Å / Num. obs: 22088 / % possible obs: 99.3 % / Redundancy: 5.9 % / CC1/2: 0.997 / Net I/σ(I): 15.5
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 3.9 % / Num. unique obs: 5668 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTV4.0data extraction
Aimless0.7.7data scaling
PHENIX1.20.1phasing
DIALS3.14.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→52.2 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1177 5.33 %
Rwork0.1696 --
obs0.1727 22065 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 96 147 4411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d8.852624
X-RAY DIFFRACTIONf_chiral_restr0.052691
X-RAY DIFFRACTIONf_plane_restr0.008775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.430.30841250.19152462X-RAY DIFFRACTION94
2.43-2.550.28381490.19412626X-RAY DIFFRACTION100
2.55-2.710.29871210.20532624X-RAY DIFFRACTION100
2.71-2.920.26631240.20152649X-RAY DIFFRACTION100
2.92-3.220.26431550.19192613X-RAY DIFFRACTION100
3.22-3.680.19571890.16732586X-RAY DIFFRACTION100
3.68-4.640.20121550.13872653X-RAY DIFFRACTION100
4.64-52.20.18461590.14962675X-RAY DIFFRACTION100

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