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- PDB-7a3w: Structure of Imine Reductase from Pseudomonas sp. -

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Basic information

Entry
Database: PDB / ID: 7a3w
TitleStructure of Imine Reductase from Pseudomonas sp.
ComponentsNAD(P)-dependent oxidoreductase
KeywordsOXIDOREDUCTASE / Imine / enimine / NADPH
Function / homologyChem-NDP
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsCuetos, A. / Thorpe, T. / Turner, N.J. / Grogan, G.
CitationJournal: Nature / Year: 2022
Title: Multifunctional biocatalyst for conjugate reduction and reductive amination.
Authors: Thorpe, T.W. / Marshall, J.R. / Harawa, V. / Ruscoe, R.E. / Cuetos, A. / Finnigan, J.D. / Angelastro, A. / Heath, R.S. / Parmeggiani, F. / Charnock, S.J. / Howard, R.M. / Kumar, R. / ...Authors: Thorpe, T.W. / Marshall, J.R. / Harawa, V. / Ruscoe, R.E. / Cuetos, A. / Finnigan, J.D. / Angelastro, A. / Heath, R.S. / Parmeggiani, F. / Charnock, S.J. / Howard, R.M. / Kumar, R. / Daniels, D.S.B. / Grogan, G. / Turner, N.J.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)-dependent oxidoreductase
B: NAD(P)-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9187
Polymers62,2112
Non-polymers1,7075
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-99 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.440, 65.391, 81.877
Angle α, β, γ (deg.)90.000, 91.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 7 - 293 / Label seq-ID: 7 - 293

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein NAD(P)-dependent oxidoreductase


Mass: 31105.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: HGP31_19350 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris buffer pH 6.5, 25% (w/v) PEG (polyethylene glycol) 3350 and 5 mM NADP+.

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.59→81.85 Å / Num. obs: 57157 / % possible obs: 83 % / Redundancy: 4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Net I/σ(I): 12.3
Reflection shellResolution: 1.59→1.62 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3245 / CC1/2: 0.85 / Rpim(I) all: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOD

6eod


Resolution: 1.59→81.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.15 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2301 2852 5 %RANDOM
Rwork0.1898 ---
obs0.1918 54283 83.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.87 Å2 / Biso mean: 20.877 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å2-0 Å20.05 Å2
2--3.3 Å20 Å2
3----1.56 Å2
Refinement stepCycle: final / Resolution: 1.59→81.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 110 324 4664
Biso mean--23.06 30.4 -
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134577
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174136
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.6336257
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5699592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56223.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61215682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4611516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
Refine LS restraints NCS

Ens-ID: 1 / Number: 9001 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.59→1.631 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 235 -
Rwork0.313 4565 -
all-4800 -
obs--94.86 %

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