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- PDB-7xg5: Crystal structure of an (R)-selective omega-transaminase mutant f... -

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Basic information

Entry
Database: PDB / ID: 7xg5
TitleCrystal structure of an (R)-selective omega-transaminase mutant from Aspergillus terreus with PLP
Componentsomega-transaminase
KeywordsTRANSFERASE / alpha/beta dehydrogenase
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
PYRIDOXAL-5'-PHOSPHATE / D-aminoacid aminotransferase-like PLP-dependent enzyme
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,0784
Polymers71,5842
Non-polymers4942
Water15,799877
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-28 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.405, 137.818, 117.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 2 - 322 / Label seq-ID: 2 - 322

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein omega-transaminase


Mass: 35792.090 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: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
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: Dec 20, 2020
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→29.36 Å / Num. obs: 83864 / % possible obs: 98.9 % / Redundancy: 13.201 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.167 / Χ2: 0.841 / Net I/σ(I): 13.87 / Num. measured all: 1107124
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
1.76-1.8712.0581.0142.4715278913585126710.8571.05893.3
1.87-214.2170.644.5218137012757127570.9440.664100
2-2.1614.0750.4017.5216762311909119090.9750.416100
2.16-2.3713.8730.27311.1615248110991109910.9870.283100
2.37-2.6413.3370.21913.74132862996299620.9890.228100
2.64-3.0512.3660.15518.49109055881988190.9940.162100
3.05-3.7311.4450.09726.7585795749674960.9970.102100
3.73-5.2713.4860.06838.6579190587258720.9980.071100
5.27-29.3613.5690.06239.6545959339433870.9990.06499.8

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Processing

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

4ce5


Resolution: 1.76→29.36 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 2000 2.39 %
Rwork0.1597 81822 -
obs0.1603 83822 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.95 Å2 / Biso mean: 23.0818 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.76→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 32 877 5896
Biso mean--16.43 34.24 -
Num. residues----642
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1985X-RAY DIFFRACTION4.017TORSIONAL
12B1985X-RAY DIFFRACTION4.017TORSIONAL
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 (%)
1.76-1.830.27041790.23787314749389
1.83-1.90.22892000.20381768376100
1.9-1.990.23292000.189881908390100
1.99-2.090.19162010.156982178418100
2.09-2.220.17512000.152882308430100
2.22-2.390.18022020.154782388440100
2.39-2.640.18752020.161582608462100
2.64-3.020.17992030.1682908493100
3.02-3.80.1652040.147683548558100
3.8-29.360.1612090.149185538762100

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