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- PDB-6skx: Structure of Reductive Aminase from Neosartorya fumigata -

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Basic information

Entry
Database: PDB / ID: 6skx
TitleStructure of Reductive Aminase from Neosartorya fumigata
ComponentsOxidoreductase, putative
KeywordsOXIDOREDUCTASE / Amine / Imine / NADPH
Function / homology
Function and homology information


3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase activity / transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / 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
Oxidoreductase, putative
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M006832/1 United Kingdom
CitationJournal: Chem Sci / Year: 2020
Title: Asymmetric synthesis of primary amines catalyzed by thermotolerant fungal reductive aminases.
Authors: Mangas-Sanchez, J. / Sharma, M. / Cosgrove, S.C. / Ramsden, J.I. / Marshall, J.R. / Thorpe, T.W. / Palmer, R.B. / Grogan, G. / Turner, N.J.
History
DepositionAug 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, putative


Theoretical massNumber of molelcules
Total (without water)30,0351
Polymers30,0351
Non-polymers00
Water79344
1
A: Oxidoreductase, putative

A: Oxidoreductase, putative


Theoretical massNumber of molelcules
Total (without water)60,0712
Polymers60,0712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area7640 Å2
ΔGint-85 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.000, 114.000, 60.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Oxidoreductase, putative


Mass: 30035.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G01250 / Plasmid: pET-YSBLIC-3C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4WDZ8, 3-hydroxyisobutyrate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris-HCl pH 7.5; 3 M NaCl;

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.25→98.73 Å / Num. obs: 21645 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.025 / Net I/σ(I): 17.4
Reflection shellResolution: 2.25→2.32 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3 / Num. unique obs: 1994 / CC1/2: 0.96 / Rpim(I) all: 0.37

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOD

6eod


Resolution: 2.25→98.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.378 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.172
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1116 5.2 %RANDOM
Rwork0.2003 ---
obs0.2022 20469 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.75 Å2 / Biso mean: 56.85 Å2 / Biso min: 37.93 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å21.18 Å20 Å2
2--2.36 Å2-0 Å2
3----7.65 Å2
Refinement stepCycle: final / Resolution: 2.25→98.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 0 44 2070
Biso mean---53.9 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132062
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171906
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6152798
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5644396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03223.24777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.646156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
LS refinement shellResolution: 2.25→2.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 91 -
Rwork0.316 1513 -
all-1604 -
obs--99.57 %

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