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- PDB-9jmy: Crystal structure of IRED in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 9jmy
TitleCrystal structure of IRED in complex with NADPH
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
Chem-NDP / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesAmycolatopsis thermoflava (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 22, 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

Downloads & links

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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)62,3659
Polymers60,3932
Non-polymers1,9737
Water3,351186
1
A: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase-like beta-hydroxyacid dehydrogenase
hetero molecules

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)124,73118
Polymers120,7854
Non-polymers3,94614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area29810 Å2
ΔGint-231 kcal/mol
Surface area35120 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13160 Å2
ΔGint-87 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.831, 75.831, 157.008
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-305-

CA

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 30196.250 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 193 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 43 %
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: Oct 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.15→36.88 Å / Num. obs: 29044 / % possible obs: 99.3 % / Redundancy: 5.64 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.12
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.2127 / Num. unique obs: 1159 / % possible all: 97.6

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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: 2.15→36.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.549 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24301 1288 4.6 %RANDOM
Rwork0.17449 ---
obs0.17744 27005 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 2.15→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 125 186 4519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174111
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6416033
X-RAY DIFFRACTIONr_angle_other_deg1.3431.5689457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66720.874206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72515640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7841534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
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_it1.8412.7242270
X-RAY DIFFRACTIONr_mcbond_other1.8412.7232269
X-RAY DIFFRACTIONr_mcangle_it2.684.0792834
X-RAY DIFFRACTIONr_mcangle_other2.6794.0792835
X-RAY DIFFRACTIONr_scbond_it2.3292.9952148
X-RAY DIFFRACTIONr_scbond_other2.3262.9942146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5394.3763200
X-RAY DIFFRACTIONr_long_range_B_refined4.87333.0684980
X-RAY DIFFRACTIONr_long_range_B_other4.87333.0674981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 93 -
Rwork0.213 1739 -
obs--86.33 %

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