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- PDB-5g6r: Imine reductase from Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 5g6r
TitleImine reductase from Aspergillus oryzae
ComponentsIMINE REDUCTASE
KeywordsOXIDOREDUCTASE / IMINE REDUCTASE / NADPH / AMINE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / 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 / 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 ...: / 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
Chem-NDP / NADPH-dependent reductive aminase
Similarity search - Component
Biological speciesASPERGILLUS ORYZAE (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMan, H. / Aleku, G. / Turner, N.J. / Grogan, G.
CitationJournal: Nat Chem / Year: 2017
Title: A reductive aminase from Aspergillus oryzae.
Authors: Aleku, G.A. / France, S.P. / Man, H. / Mangas-Sanchez, J. / Montgomery, S.L. / Sharma, M. / Leipold, F. / Hussain, S. / Grogan, G. / Turner, N.J.
History
DepositionJun 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: IMINE REDUCTASE
B: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8564
Polymers62,3652
Non-polymers1,4912
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-87 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.270, 92.440, 84.510
Angle α, β, γ (deg.)90.00, 100.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.7325, -0.5992, 0.3232), (-0.5979, -0.7392, -0.1153), (0.3254, -0.1088, -0.9393)
Vector: 13.14, 21.58, -30.93)

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Components

#1: Protein IMINE REDUCTASE


Mass: 31182.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS ORYZAE (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2TW47, EC: 1.5.1.48
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.82→61.82 Å / Num. obs: 53033 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.9
Reflection shellResolution: 1.82→1.87 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A9T

5a9t


Resolution: 1.82→61.82 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.428 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22514 2539 4.8 %RANDOM
Rwork0.18517 ---
obs0.18703 50474 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.46 Å2
2---0.31 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.82→61.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4131 0 96 164 4391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194314
X-RAY DIFFRACTIONr_bond_other_d0.0070.024073
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9995893
X-RAY DIFFRACTIONr_angle_other_deg1.45739344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2645575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40125.368136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60915656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.194156
X-RAY DIFFRACTIONr_chiral_restr0.1330.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024885
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02907
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_it3.6193.7292306
X-RAY DIFFRACTIONr_mcbond_other3.6163.7262305
X-RAY DIFFRACTIONr_mcangle_it4.7685.5762879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8544.2612008
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: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 206 -
Rwork0.309 3757 -
obs--99.72 %

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