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- PDB-7wnw: Crystal structure of Imine Reductase Mutant(M5) from Actinoallote... -

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Basic information

Entry
Database: PDB / ID: 7wnw
TitleCrystal structure of Imine Reductase Mutant(M5) from Actinoalloteichus hymeniacidonis in complex with NADPH
Components3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / Imine Reductase / NADPH / IRED
Function / homology
Function and homology information


organic acid catabolic process / NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesActinoalloteichus hymeniacidonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsZhand, J. / Chen, R. / Gao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)NSF:31872614 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Tuning an Imine Reductase for the Asymmetric Synthesis of Azacycloalkylamines by Concise Structure-Guided Engineering.
Authors: Zhang, J. / Liao, D. / Chen, R. / Zhu, F. / Ma, Y. / Gao, L. / Qu, G. / Cui, C. / Sun, Z. / Lei, X. / Gao, S.S.
History
DepositionJan 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 8, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
A: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0084
Polymers70,5212
Non-polymers1,4872
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-99 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.555, 62.444, 93.316
Angle α, β, γ (deg.)90.000, 96.753, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-647-

HOH

21B-648-

HOH

31A-590-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: givenMatrix: (-0.0894983784118, -0.991112501302, 0.0984177322674), (-0.989070171147, 0.0768165455724, -0.125854737191), (0.117176093163, -0.108605838192, -0.987154767553)Vector: -49. ...NCS oper: (Code: given
Matrix: (-0.0894983784118, -0.991112501302, 0.0984177322674), (-0.989070171147, 0.0768165455724, -0.125854737191), (0.117176093163, -0.108605838192, -0.987154767553)
Vector: -49.1920397286, -42.0559138619, 26.8432666575)

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Components

#1: Protein 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase / Imine Reductase


Mass: 35260.660 Da / Num. of mol.: 2
Mutation: N101T,G125K,H169A,L177I,F187I,M218A,S240F,M244H,A247H,N251K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoalloteichus hymeniacidonis (bacteria)
Gene: BKA25_002661 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D8BXU6
#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.: 251 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.25M ammonium sulfate, 0.1M MES buffer pH 6.0, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.13→31.22 Å / Num. obs: 38516 / % possible obs: 99.14 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.98 Å2 / CC1/2: 0.924 / Net I/σ(I): 4.31
Reflection shellResolution: 2.13→2.21 Å / Mean I/σ(I) obs: 2.21 / Num. unique obs: 3792 / CC1/2: 0.231

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WNN

7wnn


Resolution: 2.13→31.22 Å / SU ML: 0.2917 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2596 1855 4.82 %
Rwork0.2033 36661 -
obs0.206 38516 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 2.13→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4264 0 96 251 4611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694455
X-RAY DIFFRACTIONf_angle_d0.89676100
X-RAY DIFFRACTIONf_chiral_restr0.0512716
X-RAY DIFFRACTIONf_plane_restr0.0072782
X-RAY DIFFRACTIONf_dihedral_angle_d5.5635628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.31051350.26182703X-RAY DIFFRACTION95.39
2.18-2.250.34511280.25122764X-RAY DIFFRACTION98.53
2.25-2.320.28331560.24232818X-RAY DIFFRACTION98.64
2.32-2.40.32091290.23152795X-RAY DIFFRACTION98.82
2.4-2.50.30681440.23092816X-RAY DIFFRACTION99.23
2.5-2.610.28921430.22442822X-RAY DIFFRACTION99.1
2.61-2.750.30031340.21782802X-RAY DIFFRACTION99.22
2.75-2.920.31531610.22082809X-RAY DIFFRACTION99.43
2.92-3.150.24371530.20782811X-RAY DIFFRACTION99.63
3.15-3.470.24961440.20372857X-RAY DIFFRACTION99.6
3.47-3.970.22481320.17662848X-RAY DIFFRACTION99.73
3.97-4.990.20951380.17262877X-RAY DIFFRACTION99.7
5-31.220.23391580.18442939X-RAY DIFFRACTION99.77

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