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- PDB-8jku: Ancestral imine reductase N559 -

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Basic information

Entry
Database: PDB / ID: 8jku
TitleAncestral imine reductase N559
ComponentsAncestral imine reductase N559
KeywordsDE NOVO PROTEIN / ancestral protein / NADPH-dependent oxidoreductase
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsZhu, X.X. / Zheng, G.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2024
Title: Evolutionary insights into the stereoselectivity of imine reductases based on ancestral sequence reconstruction.
Authors: Zhu, X.X. / Zheng, W.Q. / Xia, Z.W. / Chen, X.R. / Jin, T. / Ding, X.W. / Chen, F.F. / Chen, Q. / Xu, J.H. / Kong, X.D. / Zheng, G.W.
History
DepositionJun 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Dec 11, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral imine reductase N559
B: Ancestral imine reductase N559
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2084
Polymers61,7222
Non-polymers1,4872
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-89 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.676, 76.167, 104.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ancestral imine reductase N559


Mass: 30860.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#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.: 56 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: PEG 3350, sodium chloride, Bis-tris

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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: May 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.57→61.65 Å / Num. obs: 21985 / % possible obs: 97 % / Redundancy: 3.1 % / CC1/2: 0.993 / Net I/σ(I): 10.2
Reflection shellResolution: 2.57→8.12 Å / Num. unique obs: 18223 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIXV1.20.1_4487refinement
XDSv0.7.7data scaling
XDSv0.7.7data reduction
PHENIXV1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→61.65 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 895 4.93 %
Rwork0.1969 --
obs0.1999 18150 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→61.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 96 56 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d9.372644
X-RAY DIFFRACTIONf_chiral_restr0.037690
X-RAY DIFFRACTIONf_plane_restr0.006762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.730.3631430.26992869X-RAY DIFFRACTION97
2.73-2.940.32661580.25962860X-RAY DIFFRACTION98
2.94-3.240.31721350.25282906X-RAY DIFFRACTION97
3.24-3.70.26731650.19862877X-RAY DIFFRACTION97
3.7-4.660.20641500.16092842X-RAY DIFFRACTION95
4.67-61.650.23351440.16832901X-RAY DIFFRACTION92

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