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- PDB-5a9r: Apo form of Imine reductase from Amycolatopsis orientalis -

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Basic information

Entry
Database: PDB / ID: 5a9r
TitleApo form of Imine reductase from Amycolatopsis orientalis
ComponentsIMINE REDUCTASE
KeywordsOXIDOREDUCTASE / IMINE REDUCTASE / NADPH / AMINE
Function / homology
Function and homology information


NADP binding / oxidoreductase activity / metal ion 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 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / NADPH-dependent reductive aminase-like, C-terminal domain / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative dehydrogenase
Similarity search - Component
Biological speciesAMYCOLATOPSIS ORIENTALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMan, H. / Aleku, G. / Turner, N.J. / Grogan, G.
CitationJournal: Acs Catalysis / Year: 2016
Title: Stereoselectivity and Structural Characterization of an Imine Reductase (Ired) from Amycolatopsis Orientalis
Authors: Aleku, G.A. / Man, H. / France, S.P. / Leipold, F. / Hussain, S. / Toca-Gonzalez, L. / Marchington, R. / Hart, S. / Turkenburg, J.P. / Grogan, G. / Turner, N.J.
History
DepositionJul 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5502
Polymers30,4911
Non-polymers591
Water1,820101
1
A: IMINE REDUCTASE
hetero molecules

A: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0994
Polymers60,9812
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8270 Å2
ΔGint-79.3 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.580, 89.620, 91.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2048-

HOH

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Components

#1: Protein IMINE REDUCTASE


Mass: 30490.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4SNK4, EC: 1.5.1.48
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M CALCIUM ACETATE, 0.1 M TRIS PH 9.0, 8% (W/V) PEG 550 MME, 8% (W/V) PEG 20K WITH PROTEIN AT A CONCENTRATION OF 20 MG PER ML

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→57.78 Å / Num. obs: 44372 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.4
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZGY

3zgy


Resolution: 1.55→57.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.55 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21378 2193 4.9 %RANDOM
Rwork0.1808 ---
obs0.18243 42178 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.417 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--1.56 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 1.55→57.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 4 101 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192141
X-RAY DIFFRACTIONr_bond_other_d0.0020.022036
X-RAY DIFFRACTIONr_angle_refined_deg2.1151.9682927
X-RAY DIFFRACTIONr_angle_other_deg1.22834667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.72123.92479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40515312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.031511
X-RAY DIFFRACTIONr_chiral_restr0.1840.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212477
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02462
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_it2.12.3161148
X-RAY DIFFRACTIONr_mcbond_other2.0562.3121146
X-RAY DIFFRACTIONr_mcangle_it2.8473.4691433
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.752.737993
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 147 -
Rwork0.247 3032 -
obs--96.42 %

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