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- PDB-5g6s: Imine reductase from Aspergillus oryzae in complex with NADP(H) a... -

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Basic information

Entry
Database: PDB / ID: 5g6s
TitleImine reductase from Aspergillus oryzae in complex with NADP(H) and (R)-rasagiline
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 / RASAGILINE / NADPH-dependent reductive aminase
Similarity search - Component
Biological speciesASPERGILLUS ORYZAE (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
C: IMINE REDUCTASE
D: IMINE REDUCTASE
E: IMINE REDUCTASE
F: IMINE REDUCTASE
G: IMINE REDUCTASE
H: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,79424
Polymers249,4618
Non-polymers7,33316
Water9,548530
1
A: IMINE REDUCTASE
G: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1996
Polymers62,3652
Non-polymers1,8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-99.4 kcal/mol
Surface area20540 Å2
MethodPISA
2
D: IMINE REDUCTASE
F: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1996
Polymers62,3652
Non-polymers1,8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-99.3 kcal/mol
Surface area20410 Å2
MethodPISA
3
E: IMINE REDUCTASE
H: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1996
Polymers62,3652
Non-polymers1,8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-97.7 kcal/mol
Surface area20340 Å2
MethodPISA
4
B: IMINE REDUCTASE
C: IMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1996
Polymers62,3652
Non-polymers1,8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-98.8 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.822, 80.255, 123.895
Angle α, β, γ (deg.)108.75, 108.78, 90.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9879, 0.00049, 0.1551), (-0.002068, 0.9999, -0.01633), (-0.1551, -0.01645, -0.9878)-32.78, -37.47, 30.01
2given(-1, -0.000194, -0.002285), (0.00019, -1, 0.001484), (-0.002285, 0.001484, 1)-30.37, 13.26, -0.01829
3given(-0.00054, 1, -0.003039), (-1, -0.000542, -0.000427), (-0.000428, 0.003039, 1)-21.69, -48.39, -55.13
4given(0.000563, -1, 0.000492), (1, 0.000563, -0.001255), (0.001255, 0.000493, 1)-8.332, -17.93, -55.18
5given(-0.002013, 0.9879, 0.1552), (0.9999, 0.004302, -0.01441), (-0.0149, 0.1552, -0.9878)-32.96, 25.13, 84.84
6given(0.9877, 2.0E-5, 0.1565), (0.002307, -0.9999, -0.01444), (0.1564, 0.01462, -0.9876)-2.761, -24.09, 34.51
7given(0.001547, -0.9874, 0.1585), (-0.9999, -0.003823, -0.01405), (0.01448, -0.1585, -0.9873)-19.73, -5.256, 87.46

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Components

#1: Protein
IMINE REDUCTASE


Mass: 31182.617 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-RAU / RASAGILINE


Mass: 171.238 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H13N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.35→75.48 Å / Num. obs: 111053 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 2.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.2 / % possible all: 97.1

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Processing

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

5a9t


Resolution: 2.35→110.32 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.443 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22902 5656 5.1 %RANDOM
Rwork0.20431 ---
obs0.20563 105360 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å2-0.32 Å2-0.42 Å2
2--0.69 Å2-0.25 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.35→110.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16864 0 488 530 17882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01917694
X-RAY DIFFRACTIONr_bond_other_d0.0070.0216836
X-RAY DIFFRACTIONr_angle_refined_deg1.7012.00624116
X-RAY DIFFRACTIONr_angle_other_deg1.3493.00238742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43652305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51425.71599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.965152811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7181525
X-RAY DIFFRACTIONr_chiral_restr0.0940.22887
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219892
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023719
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_it2.3533.7699232
X-RAY DIFFRACTIONr_mcbond_other2.3523.7699231
X-RAY DIFFRACTIONr_mcangle_it3.5765.6511527
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.774.0258462
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: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 463 -
Rwork0.305 7731 -
obs--97.04 %

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