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- PDB-6fte: Crystal structure of an (R)-selective amine transaminase from Exo... -

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Basic information

Entry
Database: PDB / ID: 6fte
TitleCrystal structure of an (R)-selective amine transaminase from Exophiala xenobiotica
ComponentsAmine transaminase (fold IV)
KeywordsBIOSYNTHETIC PROTEIN / transaminase
Function / homology
Function and homology information


carboxylic acid biosynthetic process / catalytic activity
Similarity search - Function
: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 ...: / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / Branched-chain amino acid aminotransferase
Similarity search - Component
Biological speciesExophiala xenobiotica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsTelzerow, A. / Hakansson, M. / Schurrmann, M. / Schwab, H. / Steiner, K.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Union H2020634200 Sweden
CitationJournal: Acs Catalysis / Year: 2018
Title: Amine Transaminase from Exophiala xenobiotica - Crystal Structure and Engineering of a Fold IV Transaminase that Naturally Converts Biaryl Ketones
Authors: Telzerow, A. / Paris, J. / Hakansson, M. / Gonzalez-Sabin, J. / Rios-Lombardia, N. / Schurrmann, M. / Groger, H. / Kourist, R. / Schwab, H. / Steiner, K.
History
DepositionFeb 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Structure summary / Category: struct / Item: _struct.pdbx_descriptor
Revision 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
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
B: Amine transaminase (fold IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8635
Polymers37,3731
Non-polymers4904
Water5,639313
1
B: Amine transaminase (fold IV)
hetero molecules

B: Amine transaminase (fold IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,72610
Polymers74,7452
Non-polymers9818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6970 Å2
ΔGint-29 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.431, 148.452, 78.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-523-

HOH

21B-533-

HOH

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Components

#1: Protein Amine transaminase (fold IV)


Mass: 37372.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exophiala xenobiotica (fungus) / Gene: PV05_00535 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D2C5V9
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: 2 M Ammoniumsulphate, 0.1 M Sodium acetate pH 4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 47608 / % possible obs: 100 % / Redundancy: 3.2 % / Rpim(I) all: 0.059 / Rsym value: 0.09 / Net I/σ(I): 8.8
Reflection shellResolution: 1.525→1.565 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.065 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18589 2407 5.1 %RANDOM
Rwork0.1382 ---
obs0.14062 45172 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.97 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.52→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 31 313 2865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192661
X-RAY DIFFRACTIONr_bond_other_d0.0020.022482
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9723603
X-RAY DIFFRACTIONr_angle_other_deg1.06835756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42123.879116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0311518
X-RAY DIFFRACTIONr_chiral_restr0.1190.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212972
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02551
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_it1.8451.2971314
X-RAY DIFFRACTIONr_mcbond_other1.8251.2921312
X-RAY DIFFRACTIONr_mcangle_it2.1361.9441650
X-RAY DIFFRACTIONr_mcangle_other2.1441.9461651
X-RAY DIFFRACTIONr_scbond_it2.981.6281347
X-RAY DIFFRACTIONr_scbond_other2.9791.6291348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1592.2981954
X-RAY DIFFRACTIONr_long_range_B_refined3.24616.4173073
X-RAY DIFFRACTIONr_long_range_B_other3.25216.4313074
X-RAY DIFFRACTIONr_rigid_bond_restr3.15135142
X-RAY DIFFRACTIONr_sphericity_free18.115191
X-RAY DIFFRACTIONr_sphericity_bonded7.21655204
LS refinement shellResolution: 1.525→1.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 180 -
Rwork0.252 3172 -
obs--94.26 %

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