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- PDB-9r7a: Imine Reductase IR91 from Kribbella flavida with NADP+ and 5-meth... -

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Basic information

Entry
Database: PDB / ID: 9r7a
TitleImine Reductase IR91 from Kribbella flavida with NADP+ and 5-methoxy-(S)-2-(N-methylamino)tetralin
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: 1.91 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

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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)63,8238
Polymers61,7622
Non-polymers2,0616
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-121 kcal/mol
Surface area18880 Å2
Unit cell
Length a, b, c (Å)51.800, 109.510, 53.750
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1JDG / (2~{S})-5-methoxy-~{N}-methyl-1,2,3,4-tetrahydronaphthalen-2-amine


Mass: 191.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
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; 0.2 M (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: 1.91→109.51 Å / Num. obs: 46333 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.06 / Net I/σ(I): 7.6
Reflection shellResolution: 1.91→1.95 Å / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1 / Num. unique obs: 3079 / CC1/2: 0.78 / Rpim(I) all: 0.42

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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: 1.91→54.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.968 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23533 2254 4.9 %RANDOM
Rwork0.1876 ---
obs0.1898 44044 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: 26.265 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å2-0 Å2-1.6 Å2
2---2.55 Å20 Å2
3---4.43 Å2
Refinement stepCycle: 1 / Resolution: 1.91→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 134 352 4671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164096
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6626043
X-RAY DIFFRACTIONr_angle_other_deg0.4821.5669394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.4415.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4110605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
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_it2.5882.7922322
X-RAY DIFFRACTIONr_mcbond_other2.5882.7922322
X-RAY DIFFRACTIONr_mcangle_it3.6865.0122899
X-RAY DIFFRACTIONr_mcangle_other3.6855.0122900
X-RAY DIFFRACTIONr_scbond_it3.1622.9582078
X-RAY DIFFRACTIONr_scbond_other3.1182.9422071
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6345.3083133
X-RAY DIFFRACTIONr_long_range_B_refined6.21529.015135
X-RAY DIFFRACTIONr_long_range_B_other6.10527.975053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 152 -
Rwork0.3 3234 -
obs--99.97 %

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