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- PDB-8xiy: Crystal structure of an omega-transaminase mutant I77L/Q97E/H210N... -

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Basic information

Entry
Database: PDB / ID: 8xiy
TitleCrystal structure of an omega-transaminase mutant I77L/Q97E/H210N/N245D from Aspergillus terreus in complex with PLP
ComponentsD-aminoacid aminotransferase-like PLP-dependent enzyme
KeywordsTRANSFERASE / omega-transaminase / furfuramine / TRANSLOCASE
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 NIH2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLu, Z.Y. / Hu, D. / Xu, D.Z. / He, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21978072 China
CitationJournal: To Be Published
Title: Efficient bioamination with an omega-transaminase mutant from Aspergillus terreus
Authors: He, Y.C.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-aminoacid aminotransferase-like PLP-dependent enzyme
B: D-aminoacid aminotransferase-like PLP-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2504
Polymers74,7552
Non-polymers4942
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.420, 135.790, 116.930
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
11A-753-

HOH

21B-741-

HOH

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Components

#1: Protein D-aminoacid aminotransferase-like PLP-dependent enzyme


Mass: 37377.656 Da / Num. of mol.: 2 / Mutation: I77L,Q97E,H210N,N245D
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL-5-PHOSPHATE (three-letter code PLP / Source: (gene. exp.) Aspergillus terreus NIH2624 (mold) / Gene: ATEG_10023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0C8G1
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM citrate buffer (pH 7.5) 200 mM ammonium acetate 4% (w/v) PEG-MME 8000 1 mM pyridoxal phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.09→41.881 Å / Num. obs: 49080 / % possible obs: 97.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Net I/σ(I): 16.4
Reflection shellResolution: 2.09→9.35 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3025 / Rpim(I) all: 0.441 / Rrim(I) all: 0.987 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→41.881 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2416 4.93 %
Rwork0.1711 --
obs0.1733 49044 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→41.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 32 497 5515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085132
X-RAY DIFFRACTIONf_angle_d0.8186980
X-RAY DIFFRACTIONf_dihedral_angle_d12.193038
X-RAY DIFFRACTIONf_chiral_restr0.056774
X-RAY DIFFRACTIONf_plane_restr0.006902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.13270.30321170.26952263X-RAY DIFFRACTION81
2.1327-2.17910.30141230.24882415X-RAY DIFFRACTION87
2.1791-2.22970.2891430.22882561X-RAY DIFFRACTION92
2.2297-2.28550.24161280.21622667X-RAY DIFFRACTION96
2.2855-2.34730.27251450.19552799X-RAY DIFFRACTION99
2.3473-2.41630.24921670.1892741X-RAY DIFFRACTION100
2.4163-2.49430.25321310.18552804X-RAY DIFFRACTION100
2.4943-2.58350.21751530.17822790X-RAY DIFFRACTION100
2.5835-2.68690.26261610.17552810X-RAY DIFFRACTION100
2.6869-2.80920.23991310.17812808X-RAY DIFFRACTION100
2.8092-2.95720.22351290.18152833X-RAY DIFFRACTION100
2.9572-3.14240.19451460.16462806X-RAY DIFFRACTION100
3.1424-3.3850.22141200.15872851X-RAY DIFFRACTION100
3.385-3.72540.19681510.14962827X-RAY DIFFRACTION100
3.7254-4.2640.1821550.13752837X-RAY DIFFRACTION100
4.264-5.37050.17291620.1432850X-RAY DIFFRACTION99
5.3705-41.880.2121540.18612966X-RAY DIFFRACTION100

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