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- PDB-9fm8: Imine Reductase from Rhodococcus erythropolis -

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Basic information

Entry
Database: PDB / ID: 9fm8
TitleImine Reductase from Rhodococcus erythropolis
ComponentsNAD(P)-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / NADPH / NADH / Imine Reductase / Dehydrogenase
Function / homology:
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsDomenech, J. / Jongkind, E.P.J. / Paul, C.E. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2025
Title: Discovery and Synthetic Applications of a NAD(P)H-Dependent Reductive Aminase from Rhodococcus erythropolis .
Authors: Jongkind, E.P.J. / Domenech, J. / Govers, A. / van den Broek, M. / Daran, J.M. / Grogan, G. / Paul, C.E.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)30,6431
Polymers30,6431
Non-polymers00
Water43224
1
A: NAD(P)-dependent oxidoreductase

A: NAD(P)-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)61,2862
Polymers61,2862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area9050 Å2
ΔGint-72 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.660, 80.660, 82.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NAD(P)-dependent oxidoreductase


Mass: 30643.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: EHW12_26885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G9A570
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M bis Tris propane pH 5.5; 0.2 M MgCl2; 25% PEG 3350

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 97627 Å / Relative weight: 1
ReflectionResolution: 2.38→53.44 Å / Num. obs: 12900 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 47 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.03 / Net I/σ(I): 8.6
Reflection shellResolution: 2.38→2.47 Å / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1319 / CC1/2: 0.96 / Rpim(I) all: 0.22

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→53.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.461 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29968 705 5.5 %RANDOM
Rwork0.21756 ---
obs0.22179 12169 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.858 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å21.58 Å20 Å2
2--3.15 Å2-0 Å2
3----10.23 Å2
Refinement stepCycle: 1 / Resolution: 2.38→53.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 0 24 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161910
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.7642853
X-RAY DIFFRACTIONr_angle_other_deg0.521.7164349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4185285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.901510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86510285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022576
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
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_it6.1217.1281143
X-RAY DIFFRACTIONr_mcbond_other6.127.1281143
X-RAY DIFFRACTIONr_mcangle_it9.09512.7981427
X-RAY DIFFRACTIONr_mcangle_other9.09212.8021428
X-RAY DIFFRACTIONr_scbond_it6.0337.461944
X-RAY DIFFRACTIONr_scbond_other6.037.465945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.313.551427
X-RAY DIFFRACTIONr_long_range_B_refined11.77669.972417
X-RAY DIFFRACTIONr_long_range_B_other11.77469.752417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 72 -
Rwork0.387 871 -
obs--99.58 %

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