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- PDB-9h4f: Structure of Imine Reductase 361 from Micromonospora sp. mutant M... -

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Basic information

Entry
Database: PDB / ID: 9h4f
TitleStructure of Imine Reductase 361 from Micromonospora sp. mutant M125W/I127F/L179V/H250L
Components6-phosphogluconate dehydrogenase
KeywordsOXIDOREDUCTASE / Amine / NADP
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
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
Similarity search - Component
Biological speciesMicromonospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsHo, E. / Domenech, J. / Crossley, A. / Green, A.P. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Engineered Biocatalyst for Enantioselective Hydrazone Reduction.
Authors: Hutton, A.E. / Zhao, F. / Ho, E. / Domenech, J. / Harawa, V. / Brown, M.J.B. / Grogan, G. / Clayman, P.D. / Turner, N.J. / Green, A.P.
History
DepositionOct 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 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
B: 6-phosphogluconate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9733
Polymers63,2292
Non-polymers7431
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-94 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.268, 184.268, 184.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein 6-phosphogluconate dehydrogenase


Mass: 31614.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora (bacteria) / Gene: BSA16_00815 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S8Y2S4
#2: 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
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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate in bis-Tris buffer pH 6.5 with 2 mM NADP

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.77→130.3 Å / Num. obs: 15775 / % possible obs: 93.7 % / Redundancy: 40.4 % / Biso Wilson estimate: 115 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.02 / Net I/σ(I): 37.6
Reflection shellResolution: 2.77→3.34 Å / Rmerge(I) obs: 2.64 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 789 / CC1/2: 0.78 / Rpim(I) all: 0.42

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→130.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 26.872 / SU ML: 0.438 / Cross valid method: THROUGHOUT / ESU R: 3.028 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30371 708 4.5 %RANDOM
Rwork0.22578 ---
obs0.22936 15067 59.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.514 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.77→130.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 0 0 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123778
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163186
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.7575217
X-RAY DIFFRACTIONr_angle_other_deg0.5361.6857205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0585554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.41856
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69310356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024566
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02775
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_it11.74313.4892243
X-RAY DIFFRACTIONr_mcbond_other11.7413.4892243
X-RAY DIFFRACTIONr_mcangle_it17.80224.1092788
X-RAY DIFFRACTIONr_mcangle_other17.824.112789
X-RAY DIFFRACTIONr_scbond_it12.27412.7811535
X-RAY DIFFRACTIONr_scbond_other12.24812.7861535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.9223.532430
X-RAY DIFFRACTIONr_long_range_B_refined23.067123.445039
X-RAY DIFFRACTIONr_long_range_B_other23.074123.445040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.774→2.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.039 6 -
obs--0.31 %

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