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- PDB-9jmx: Crystal structure of IRED-M235A in complex with NADP+ and substrate -

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Basic information

Entry
Database: PDB / ID: 9jmx
TitleCrystal structure of IRED-M235A in complex with NADP+ and substrate
Components3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / imine reductase
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesAmycolatopsis thermoflava (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsFu, X.L. / Zhang, M.T. / Yi, S.M. / Dai, K.X. / Yang, Y.Y. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911400 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Mutagenesis of a Single Site Inverts the Stereopreference of Imine Reductase
Authors: Li, Y. / Yang, Y. / Zhang, M. / Yue, X. / Guo, R.T. / Huang, Z. / Chen, F.
History
DepositionSep 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
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.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,2126
Polymers60,2722
Non-polymers1,9394
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-88 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.753, 78.753, 160.405
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

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Components

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


Mass: 30136.133 Da / Num. of mol.: 2 / Mutation: M235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis thermoflava (bacteria) / Gene: EDD35_0917 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3N2GPT5
#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
#3: Chemical ChemComp-A1ECB / 1-~{tert}-butyl-4,9-dihydro-3~{H}-pyrido[3,4-b]indole


Mass: 226.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.03 M CaCl2, 0.1M MES pH 6.0, 49% v/v PEG 200

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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: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.04→34.59 Å / Num. obs: 37464 / % possible obs: 99.8 % / Redundancy: 7.84 % / Rmerge(I) obs: 0.0673 / Net I/σ(I): 15.37
Reflection shellResolution: 2.04→2.07 Å / Rmerge(I) obs: 0.4532 / Num. unique obs: 1591

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
SAINTdata reduction
PDB_EXTRACT2.34data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→34.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.872 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25964 1849 5 %RANDOM
Rwork0.20552 ---
obs0.2082 35441 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: 1 / Resolution: 2.04→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 130 193 4515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134416
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174093
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6826052
X-RAY DIFFRACTIONr_angle_other_deg1.3851.5979395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15920.874206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21315629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6931534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02961
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_it2.7333.6352266
X-RAY DIFFRACTIONr_mcbond_other2.733.6342265
X-RAY DIFFRACTIONr_mcangle_it3.7725.4452829
X-RAY DIFFRACTIONr_mcangle_other3.7725.4452830
X-RAY DIFFRACTIONr_scbond_it2.9183.8422150
X-RAY DIFFRACTIONr_scbond_other2.9173.8432151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3545.6573224
X-RAY DIFFRACTIONr_long_range_B_refined5.95843.085103
X-RAY DIFFRACTIONr_long_range_B_other5.95843.0775104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 113 -
Rwork0.272 2560 -
obs--98.78 %

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