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- PDB-8e9s: Crystal structure of E. coli aspartate aminotransferase mutant VF... -

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Basic information

Entry
Database: PDB / ID: 8e9s
TitleCrystal structure of E. coli aspartate aminotransferase mutant VFCS bound to maleic acid at 278 K
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / Enzyme / Designed Protein / Mutant Protein
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
MALEIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChica, R.A. / St-Jacques, A.D. / Rodriguez, J.M. / Thompson, M.C.
Funding support Canada, United States, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04831 Canada
Ontario Early Researcher AwardsER14-10-139 Canada
Canada Foundation for Innovation26503 Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124169 United States
CitationJournal: Nat Commun / Year: 2023
Title: Computational remodeling of an enzyme conformational landscape for altered substrate selectivity.
Authors: St-Jacques, A.D. / Rodriguez, J.M. / Eason, M.G. / Foster, S.M. / Khan, S.T. / Damry, A.M. / Goto, N.K. / Thompson, M.C. / Chica, R.A.
History
DepositionAug 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2656
Polymers89,5392
Non-polymers7264
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-19 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.830, 143.830, 81.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Aspartate aminotransferase / AspAT / Transaminase A


Mass: 44769.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aspC, b0928, JW0911 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#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-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, ammonium sulfate, PEG 400, maleate

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Data collection

DiffractionMean temperature: 278 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.8855 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8855 Å / Relative weight: 1
ReflectionResolution: 2→124.49 Å / Num. obs: 64724 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 27.15 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.1
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 3199 / CC1/2: 0.571

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X28

1x28


Resolution: 2→124.49 Å / SU ML: 0.2242 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.185 6535 10.1 %
Rwork0.1479 58160 -
obs0.1517 64695 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.48 Å2
Refinement stepCycle: LAST / Resolution: 2→124.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6168 0 0 343 6511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516351
X-RAY DIFFRACTIONf_angle_d0.83928636
X-RAY DIFFRACTIONf_chiral_restr0.0442951
X-RAY DIFFRACTIONf_plane_restr0.00461152
X-RAY DIFFRACTIONf_dihedral_angle_d21.70652276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.33421710.27721516X-RAY DIFFRACTION79.2
2.02-2.040.26412210.2551932X-RAY DIFFRACTION100
2.04-2.070.27332210.24681949X-RAY DIFFRACTION100
2.07-2.10.2842150.24631948X-RAY DIFFRACTION100
2.1-2.120.27172210.23211945X-RAY DIFFRACTION100
2.12-2.150.2592210.23151943X-RAY DIFFRACTION100
2.15-2.180.2832140.2141937X-RAY DIFFRACTION100
2.18-2.220.23342230.19831934X-RAY DIFFRACTION100
2.22-2.250.23872440.19181924X-RAY DIFFRACTION100
2.25-2.290.23832360.18871926X-RAY DIFFRACTION100
2.29-2.330.22762090.1761962X-RAY DIFFRACTION100
2.33-2.370.21571930.17451948X-RAY DIFFRACTION100
2.37-2.410.22672030.17411941X-RAY DIFFRACTION100
2.41-2.460.20842100.16341994X-RAY DIFFRACTION100
2.46-2.520.21172270.1551928X-RAY DIFFRACTION100
2.52-2.580.18592150.15431955X-RAY DIFFRACTION100
2.58-2.640.19612050.15591948X-RAY DIFFRACTION100
2.64-2.710.20132230.15341969X-RAY DIFFRACTION100
2.71-2.790.20812250.15871934X-RAY DIFFRACTION100
2.79-2.880.22032110.1571970X-RAY DIFFRACTION100
2.88-2.980.19292400.15361919X-RAY DIFFRACTION99.95
2.98-3.10.21432380.15291929X-RAY DIFFRACTION100
3.1-3.240.19122360.15571951X-RAY DIFFRACTION100
3.25-3.420.18812140.13661963X-RAY DIFFRACTION100
3.42-3.630.14582050.12271966X-RAY DIFFRACTION100
3.63-3.910.13382100.10421973X-RAY DIFFRACTION100
3.91-4.30.12972240.09641968X-RAY DIFFRACTION100
4.3-4.930.122320.08991958X-RAY DIFFRACTION100
4.93-6.210.14612120.12151996X-RAY DIFFRACTION100
6.21-124.490.13712160.13172034X-RAY DIFFRACTION99.6

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