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- PDB-27il: Crystal structure of Imine Reductase Mutant(R7) from Actinoallote... -

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Basic information

Entry
Database: PDB / ID: 27il
TitleCrystal structure of Imine Reductase Mutant(R7) from Actinoalloteichus hymeniacidonis in complex with NADPH
Components3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / imine reductase / NADPH-binding / mutant / enzyme engineering
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / 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: 1.92 Å
AuthorsSong, S. / Lin, L.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Crystal structure of an engineered imine reductase mutant in complex with NADPH
Authors: Song, S. / Lin, L.
History
DepositionJun 2, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)67,1174
Polymers66,3052
Non-polymers8122
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-86 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.770, 62.820, 95.012
Angle α, β, γ (deg.)90.000, 97.306, 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

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Components

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


Mass: 33152.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoalloteichus hymeniacidonis (bacteria)
Gene: BKA25_002661, TL08_13965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAC9HQB1
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M imidazole malate, 20% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.92→29.88 Å / Num. obs: 53657 / % possible obs: 98.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 28.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.043 / Rrim(I) all: 0.078 / Χ2: 0.95 / Net I/σ(I): 13.1
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.654 / Num. unique obs: 3160 / CC1/2: 0.767 / Rpim(I) all: 0.552 / Rrim(I) all: 0.841 / Χ2: 0.89 / % possible all: 86.2

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→26.52 Å / SU ML: 0.2222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 1989 3.73 %
Rwork0.1941 51290 -
obs0.1956 53279 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.26 Å2
Refinement stepCycle: LAST / Resolution: 1.92→26.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 53 246 4593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624454
X-RAY DIFFRACTIONf_angle_d0.74376088
X-RAY DIFFRACTIONf_chiral_restr0.049707
X-RAY DIFFRACTIONf_plane_restr0.0076793
X-RAY DIFFRACTIONf_dihedral_angle_d16.56831578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.36591230.33523195X-RAY DIFFRACTION84.84
1.97-2.020.36651340.28633539X-RAY DIFFRACTION95.4
2.02-2.080.28361410.25533652X-RAY DIFFRACTION98.19
2.08-2.150.29641450.22793687X-RAY DIFFRACTION99.12
2.15-2.220.28991420.24423644X-RAY DIFFRACTION98.06
2.22-2.310.3441400.2913583X-RAY DIFFRACTION95.93
2.31-2.420.24631430.20593716X-RAY DIFFRACTION99.61
2.42-2.550.23841450.19533741X-RAY DIFFRACTION99.79
2.55-2.710.25981460.18973736X-RAY DIFFRACTION99.62
2.71-2.910.241450.2033721X-RAY DIFFRACTION99.66
2.91-3.210.22191470.20073757X-RAY DIFFRACTION99.82
3.21-3.670.22481450.19273753X-RAY DIFFRACTION99.64
3.67-4.620.20121460.16143758X-RAY DIFFRACTION99.46
4.62-26.520.18221470.15533808X-RAY DIFFRACTION98.46

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