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- PDB-7xg6: Crystal structure of an (R)-selective omega-transaminase mutant f... -

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Basic information

Entry
Database: PDB / ID: 7xg6
TitleCrystal structure of an (R)-selective omega-transaminase mutant from Aspergillus terreus with covalently bound PLP
Componentsomega-transaminase
KeywordsTRANSFERASE / LLP
Function / homology
Function and homology information


aspartate biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / metal ion binding / cytosol
Similarity search - Function
Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
D-aminoacid aminotransferase-like PLP-dependent enzyme
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsXiang, C. / Wu, S.K. / Weber, G. / Liu, W.D. / Wei, R. / Bornscheuer, U.T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2022
Title: A growth selection system for the directed evolution of amine-forming or converting enzymes.
Authors: Wu, S. / Xiang, C. / Zhou, Y. / Khan, M.S.H. / Liu, W. / Feiler, C.G. / Wei, R. / Weber, G. / Hohne, M. / Bornscheuer, U.T.
History
DepositionApr 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: omega-transaminase
B: omega-transaminase


Theoretical massNumber of molelcules
Total (without water)72,0402
Polymers72,0402
Non-polymers00
Water18,1051005
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-31 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.764, 136.299, 116.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-782-

HOH

21B-870-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 98 or resid 100 through 322))
21(chain B and (resid 1 through 98 or resid 100 through 322))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 98 or resid 100 through 322))A1 - 98
121(chain A and (resid 1 through 98 or resid 100 through 322))A100 - 322
211(chain B and (resid 1 through 98 or resid 100 through 322))B1 - 98
221(chain B and (resid 1 through 98 or resid 100 through 322))B100 - 322

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Components

#1: Protein omega-transaminase


Mass: 36020.211 Da / Num. of mol.: 2 / Mutation: H55R, F115H, E117C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (strain NIH 2624 / FGSC A1156) (mold)
Strain: NIH 2624 / FGSC A1156 / Gene: ATEG_10023 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0C8G1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1005 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2021
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→39.16 Å / Num. obs: 195760 / % possible obs: 99.7 % / Redundancy: 7.447 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.073 / Χ2: 0.841 / Net I/σ(I): 17.34 / Num. measured all: 1457835
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.32-1.47.5230.6352.8623463831521311900.840.68298.9
1.4-1.57.3390.4334.1421679329651295390.9170.46699.6
1.5-1.626.7290.2676.2318557527619275780.9620.2999.9
1.62-1.777.8860.17810.320091225497254770.9880.1999.9
1.77-1.987.8540.10816.9918096623080230420.9960.11699.8
1.98-2.287.5840.06927.0115476120427204050.9980.07499.9
2.28-2.86.890.0534.7411940517336173290.9980.054100
2.8-3.957.7110.03453.0310428013529135230.9990.036100
3.95-39.167.8810.0363.5860505769876770.9990.03299.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE5

4ce5


Resolution: 1.32→39.16 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 15.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1633 2000 1.02 %
Rwork0.154 193588 -
obs0.1541 195588 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.27 Å2 / Biso mean: 16.0567 Å2 / Biso min: 7.15 Å2
Refinement stepCycle: final / Resolution: 1.32→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 0 1005 6045
Biso mean---27.82 -
Num. residues----642
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1968X-RAY DIFFRACTION5.108TORSIONAL
12B1968X-RAY DIFFRACTION5.108TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.32-1.370.23171980.2098191221932099
1.37-1.420.22321980.19111920519403100
1.42-1.490.20631980.17681921019408100
1.49-1.570.17611990.16151923619435100
1.57-1.660.16992000.1531931519515100
1.66-1.790.17421990.15371931019509100
1.79-1.970.15982000.15111933519535100
1.97-2.260.17562000.14421941719617100
2.26-2.840.16062020.15411954519747100
2.84-39.160.13542060.14411989320099100

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