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- PDB-7qyf: Structure of the transaminase PluriZyme variant (TR2E2) -

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Basic information

Entry
Database: PDB / ID: 7qyf
TitleStructure of the transaminase PluriZyme variant (TR2E2)
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
Aminotransferase TR2
Similarity search - Component
Biological speciesAcidihalobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)206,6354
Polymers206,6354
Non-polymers00
Water00
1
A: Aminotransferase TR2
D: Aminotransferase TR2


Theoretical massNumber of molelcules
Total (without water)103,3172
Polymers103,3172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-38 kcal/mol
Surface area29810 Å2
2
B: Aminotransferase TR2
C: Aminotransferase TR2


Theoretical massNumber of molelcules
Total (without water)103,3172
Polymers103,3172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-32 kcal/mol
Surface area30090 Å2
Unit cell
Length a, b, c (Å)100.358, 108.988, 212.178
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

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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
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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 200 mM calcium acetate, 100 mM HEPES pH 7.5, 10% (w/v) PEG 8000

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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: 0.9677 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: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.3→39.65 Å / Num. obs: 37886 / % possible obs: 98.45 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 7.83
Reflection shellResolution: 3.3→3.418 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 3500 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QX0

7qx0


Resolution: 3.3→39.65 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2797 --
Rwork0.226 --
obs-35219 98.45 %
Displacement parametersBiso mean: 96.81 Å2
Refinement stepCycle: LAST / Resolution: 3.3→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12929 0 0 0 12929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011813219
X-RAY DIFFRACTIONf_angle_d1.480417891
X-RAY DIFFRACTIONf_chiral_restr0.18431918
X-RAY DIFFRACTIONf_plane_restr0.00982350
X-RAY DIFFRACTIONf_dihedral_angle_d19.49874939

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