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- PDB-7qx3: Structure of the transaminase TR2E2 with EOS -

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Basic information

Entry
Database: PDB / ID: 7qx3
TitleStructure of the transaminase TR2E2 with EOS
ComponentsAminotransferase TR2
KeywordsHYDROLASE / transaminase
Function / homology
Function and homology information


beta-alanine-pyruvate transaminase / beta-alanine:pyruvate transaminase activity / gamma-aminobutyric acid metabolic process / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
2-azanylethyl hydrogen sulfate / Aminotransferase TR2
Similarity search - Component
Biological speciesAcidihalobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsRoda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G. ...Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G. / Gonzalez-Alfonso, J. / Plou, F.J. / Jaeger, K.E. / Smits, S.H. / Ferrer, M. / Guallar, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)417919780 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: A Plurizyme with Transaminase and Hydrolase Activity Catalyzes Cascade Reactions.
Authors: Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G.W. / Gonzalez-Alfonso, J.L. / Plou, F.J. ...Authors: Roda, S. / Fernandez-Lopez, L. / Benedens, M. / Bollinger, A. / Thies, S. / Schumacher, J. / Coscolin, C. / Kazemi, M. / Santiago, G. / Gertzen, C.G.W. / Gonzalez-Alfonso, J.L. / Plou, F.J. / Jaeger, K.E. / Smits, S.H.J. / Ferrer, M. / Guallar, V.
History
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Aminotransferase TR2
C: Aminotransferase TR2
A: Aminotransferase TR2
D: Aminotransferase TR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,1998
Polymers206,6354
Non-polymers5654
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.610, 109.502, 211.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.993734770954, -0.0666509067163, 0.0897154481194), (-0.0661972169224, 0.997774276484, 0.00802631034981), (-0.0900507271992, 0.00203711069662, -0.995935096636)53.9010591199, 20.1898220549, 4.8416532732
2given(0.999596559128, 0.0203915551007, 0.0197712786762), (0.0259976815124, -0.937220130977, -0.347767949425), (0.0114385110875, 0.348141653026, -0.937372151225)-13.2356166714, -18.4663514136, 7.26148910248
3given(-0.997011350258, -0.016051164773, 0.0755693560016), (-0.0114977199612, -0.936455040695, -0.35059914317), (0.0763948289661, -0.350420200425, 0.933471752782)68.4734848065, -35.1397502327, -8.90172623928
4given(-0.0103127797322, -0.475758429753, -0.879515527488), (0.129359287417, 0.871536488488, -0.472959114504), (0.991544160052, -0.118651025078, 0.052555807621)33.5854361738, 12.4674922061, -10.3978232136
5given(-0.603610600379, -0.110552047569, -0.789577410954), (0.00640431256748, 0.98963554616, -0.143458950772), (0.797253553075, -0.0916500439413, -0.596646496306)62.8921775001, -15.4739484195, -34.6851033307
6given(-0.624415100238, -0.391087373894, 0.676133454709), (-0.74812151714, 0.0505981985609, -0.661629819381), (0.224543933756, -0.918961635915, -0.324175158718)51.489763648, 31.9421883501, -21.2207519276

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Components

#1: Protein
Aminotransferase TR2


Mass: 51658.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidihalobacter (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3G5BC54, beta-alanine-pyruvate transaminase
#2: Chemical
ChemComp-GH0 / 2-azanylethyl hydrogen sulfate


Mass: 141.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7NO4S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 278 K / Method: vapor diffusion / Details: 4% (w/v) PEG 6000, 100 mM citric acid pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.6→48.94 Å / Num. obs: 27774 / % possible obs: 99.85 % / Redundancy: 13 % / Biso Wilson estimate: 72.36 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.38
Reflection shellResolution: 3.6→3.729 Å / Num. unique obs: 2733 / CC1/2: 0.977

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QX0

7qx0


Resolution: 3.6→48.94 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 --
Rwork0.1606 --
obs-27774 99.85 %
Displacement parametersBiso mean: 71.11 Å2
Refinement stepCycle: LAST / Resolution: 3.6→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13045 0 32 0 13077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01713377
X-RAY DIFFRACTIONf_angle_d1.768718104
X-RAY DIFFRACTIONf_chiral_restr0.06891924
X-RAY DIFFRACTIONf_plane_restr0.01282375
X-RAY DIFFRACTIONf_dihedral_angle_d14.99095002
LS refinement shellResolution: 3.6→3.729 Å / Rfactor Rfree: 0.2962 / Rfactor Rwork: 0.1998

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