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- PDB-8a5z: Imine Reductase from Ensifer adhaerens A208N mutant in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8a5z
TitleImine Reductase from Ensifer adhaerens A208N mutant in complex with NADP+
ComponentsNAD_binding_2 domain-containing protein
KeywordsOXIDOREDUCTASE / Amine / NADP / Imine Reductase Oxidoreductase
Function / homology
Function and homology information


cellular catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NADP 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
IODIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesEnsifer adhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsGilio, A.K. / Grogan, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: A Reductive Aminase Switches to Imine Reductase Mode for a Bulky Amine Substrate.
Authors: Gilio, A.K. / Thorpe, T.W. / Heyam, A. / Petchey, M.R. / Pogranyi, B. / France, S.P. / Howard, R.M. / Karmilowicz, M.J. / Lewis, R. / Turner, N. / Grogan, G.
History
DepositionJun 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: 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
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_binding_2 domain-containing protein
B: NAD_binding_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,79912
Polymers62,2962
Non-polymers2,50210
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.000, 89.000, 94.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 292 / Label seq-ID: 2 - 292

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

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Components

#1: Protein NAD_binding_2 domain-containing protein


Mass: 31148.242 Da / Num. of mol.: 2 / Mutation: A208N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ensifer adhaerens (bacteria) / Gene: AC244_29830 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L8BGL4
#2: 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
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 % mPEG 3350 w/v, 3% propan-1-ol v/v, 0.1 M NaI and 0.1 M bis tris propane

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 120 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.31→64.63 Å / Num. obs: 30238 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.05 / Net I/σ(I): 10.2
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2921 / CC1/2: 0.93 / Rpim(I) all: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A3X

8a3x


Resolution: 2.31→64.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.968 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 1540 5.1 %RANDOM
Rwork0.1975 ---
obs0.1998 28908 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 max: 115.5 Å2 / Biso mean: 41.676 Å2 / Biso min: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--5.62 Å20 Å2-0 Å2
2---0.99 Å20 Å2
3---6.62 Å2
Refinement stepCycle: final / Resolution: 2.31→64.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 104 162 4553
Biso mean--41.04 38.26 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154213
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.6356119
X-RAY DIFFRACTIONr_angle_other_deg1.3621.5739618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3435587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24120.19210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78115652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3641539
X-RAY DIFFRACTIONr_chiral_restr0.0740.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021038
Refine LS restraints NCS

Ens-ID: 1 / Number: 8390 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.31→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 124 -
Rwork0.339 2073 -
all-2197 -
obs--100 %

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