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- PDB-9r79: Imine Reductase IR91 from Kribbella flavida with NADP+ and 5-meth... -

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Basic information

Entry
Database: PDB / ID: 9r79
TitleImine Reductase IR91 from Kribbella flavida with NADP+ and 5-methoxy-2-tetralone
Components6-phosphogluconate dehydrogenase NAD-binding protein
KeywordsOXIDOREDUCTASE / Amine / Imine / NADPH / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 6-phosphogluconate dehydrogenase NAD-binding protein
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSrinivas, K. / Gilio, A.K. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2025
Title: Structures of "Tyrosine-IRED" IR91 from Kribbella flavida in Complex with a Reductive Amination Substrate and Product.
Authors: Srinivas, K. / Gilio, A.K. / Sharma, M. / Green, L. / Ascham, A. / Domenech, J. / Pogranyi, B. / Li, J. / France, S.P. / Lewis, R.D. / Unsworth, W.P. / Grogan, G.
History
DepositionMay 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phosphogluconate dehydrogenase NAD-binding protein
B: 6-phosphogluconate dehydrogenase NAD-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,42616
Polymers61,7622
Non-polymers2,66414
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-185 kcal/mol
Surface area18810 Å2
Unit cell
Length a, b, c (Å)51.900, 102.890, 108.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 6-phosphogluconate dehydrogenase NAD-binding protein


Mass: 30880.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Gene: Kfla_3935 / Production host: Escherichia coli (E. coli) / References: UniProt: D2PR38

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Non-polymers , 5 types, 430 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1JDH / 5-methoxy-3,4-dihydro-1~{H}-naphthalen-2-one


Mass: 176.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M btp buffer pH 5.5; 25% (w/v) PEG 3350; 0.2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.8→48.1 Å / Num. obs: 54815 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.05 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1 / Num. unique obs: 3176 / CC1/2: 0.89 / Rpim(I) all: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.242 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23939 2643 4.8 %RANDOM
Rwork0.2029 ---
obs0.20469 52100 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.061 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-0 Å2
2--3.15 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4192 0 168 416 4776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124458
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164132
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.6636111
X-RAY DIFFRACTIONr_angle_other_deg0.4481.5659487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.4575.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30110609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
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_it1.642.1022331
X-RAY DIFFRACTIONr_mcbond_other1.642.1022331
X-RAY DIFFRACTIONr_mcangle_it2.5213.7742912
X-RAY DIFFRACTIONr_mcangle_other2.5213.7742913
X-RAY DIFFRACTIONr_scbond_it2.2822.2932127
X-RAY DIFFRACTIONr_scbond_other2.1862.2582104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3554.063164
X-RAY DIFFRACTIONr_long_range_B_refined5.72224.995163
X-RAY DIFFRACTIONr_long_range_B_other5.623.285039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 170 -
Rwork0.338 3808 -
obs--99.97 %

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