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- PDB-6xu3: (R)-selective amine transaminase from Shinella sp. -

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Basic information

Entry
Database: PDB / ID: 6xu3
Title(R)-selective amine transaminase from Shinella sp.
ComponentsClass IV aminotransferase
KeywordsTRANSFERASE / fold IV PLP-dependent enzyme / amine transaminase
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
3-AMINOBENZOIC ACID / NITRATE ION / DI(HYDROXYETHYL)ETHER / Chem-PLG / PYRIDOXAL-5'-PHOSPHATE / Probable branched-chain-amino-acid aminotransferase
Similarity search - Component
Biological speciesShinella sp. JR1-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTelzerow, A. / Hakansson, M. / Steiner, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
European Commission634200 Austria
CitationJournal: Chembiochem / Year: 2021
Title: Expanding the Toolbox of R-Selective Amine Transaminases by Identification and Characterization of New Members.
Authors: Telzerow, A. / Paris, J. / Hakansson, M. / Gonzalez-Sabin, J. / Rios-Lombardia, N. / Groger, H. / Moris, F. / Schurmann, M. / Schwab, H. / Steiner, K.
History
DepositionJan 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
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: Class IV aminotransferase
B: Class IV aminotransferase
C: Class IV aminotransferase
D: Class IV aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,19323
Polymers146,9394
Non-polymers2,25319
Water11,061614
1
A: Class IV aminotransferase
D: Class IV aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50611
Polymers73,4702
Non-polymers1,0369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-19 kcal/mol
Surface area25120 Å2
MethodPISA
2
B: Class IV aminotransferase
C: Class IV aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,68712
Polymers73,4702
Non-polymers1,21710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-28 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.374, 82.118, 222.435
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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Class IV aminotransferase


Mass: 36734.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shinella sp. JR1-6 (bacteria) / Gene: EXZ48_21850 / Plasmid: pEHISTEV / Cell line (production host): BL21-Gold(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q8MG35

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Non-polymers , 8 types, 633 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P
#8: Chemical ChemComp-GAB / 3-AMINOBENZOIC ACID / GABACULINE


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium nitrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.099→46.04 Å / Num. obs: 81122 / % possible obs: 99.48 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.38 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1346 / Rpim(I) all: 0.05517 / Rrim(I) all: 0.1457 / Net I/σ(I): 10.94
Reflection shellResolution: 2.099→2.174 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.291 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 7727 / CC1/2: 0.581 / CC star: 0.857 / Rpim(I) all: 0.5618 / % possible all: 96.23

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata scaling
XDSdata reduction
PHENIX1.14-3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE5
Resolution: 2.1→46.04 Å / SU ML: 0.2739 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.1561
RfactorNum. reflection% reflection
Rfree0.2297 4189 5.17 %
Rwork0.1891 --
obs0.1913 81094 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.81 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10180 0 145 614 10939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016910649
X-RAY DIFFRACTIONf_angle_d1.641214450
X-RAY DIFFRACTIONf_chiral_restr0.08721548
X-RAY DIFFRACTIONf_plane_restr0.00611866
X-RAY DIFFRACTIONf_dihedral_angle_d15.3463931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.37411260.34292197X-RAY DIFFRACTION88.6
2.12-2.150.38431380.30512582X-RAY DIFFRACTION100
2.15-2.170.32341310.29612543X-RAY DIFFRACTION99.89
2.17-2.20.31011220.27912555X-RAY DIFFRACTION99.93
2.2-2.230.30941350.27882564X-RAY DIFFRACTION99.96
2.23-2.260.29931220.26382529X-RAY DIFFRACTION99.92
2.26-2.290.3221620.25912527X-RAY DIFFRACTION99.85
2.29-2.330.27761250.24332537X-RAY DIFFRACTION100
2.33-2.360.28991530.23262559X-RAY DIFFRACTION99.93
2.36-2.40.29581460.23882523X-RAY DIFFRACTION99.89
2.4-2.440.27891450.2482550X-RAY DIFFRACTION99.48
2.44-2.490.32081460.24232525X-RAY DIFFRACTION99.52
2.49-2.540.29351270.22162573X-RAY DIFFRACTION100
2.54-2.590.28391430.2192566X-RAY DIFFRACTION99.93
2.59-2.640.25381390.22242538X-RAY DIFFRACTION99.96
2.64-2.710.28031390.21252545X-RAY DIFFRACTION99.89
2.71-2.770.28551490.2122555X-RAY DIFFRACTION99.96
2.77-2.850.25821580.20362547X-RAY DIFFRACTION100
2.85-2.930.23181430.19252586X-RAY DIFFRACTION99.74
2.93-3.030.24781390.18692556X-RAY DIFFRACTION99.93
3.03-3.140.23231290.18472581X-RAY DIFFRACTION99.85
3.14-3.260.22541400.19512581X-RAY DIFFRACTION99.85
3.26-3.410.25061230.18662609X-RAY DIFFRACTION100
3.41-3.590.23081320.17712608X-RAY DIFFRACTION99.96
3.59-3.810.19251380.16752572X-RAY DIFFRACTION100
3.81-4.110.17651680.15572597X-RAY DIFFRACTION100
4.11-4.520.16841520.13162597X-RAY DIFFRACTION99.78
4.52-5.170.17191510.13392614X-RAY DIFFRACTION99.64
5.17-6.520.19541210.15852696X-RAY DIFFRACTION100

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