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- PDB-2qbt: Structural Studies Reveal The Inactivation of E. coli L-aspartate... -

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Basic information

Entry
Database: PDB / ID: 2qbt
TitleStructural Studies Reveal The Inactivation of E. coli L-aspartate aminotransferase by (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via Two Mechanisms (at pH 8.0)
ComponentsAspartate aminotransferase
KeywordsTRANSFERASE / mechanism-based inactivator / pH dependence / aspartate aminotransferase / SADTA / PLP
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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...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 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Chem-PSZ / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLiu, D. / Pozharski, E. / Lepore, B. / Fu, M. / Silverman, R.B. / Petsko, G.A. / Ringe, D.
CitationJournal: Biochemistry / Year: 2007
Title: Inactivation of Escherichia coli l-Aspartate Aminotransferase by (S)-4-Amino-4,5-dihydro-2-thiophenecarboxylic Acid Reveals "A Tale of Two Mechanisms".
Authors: Liu, D. / Pozharski, E. / Lepore, B.W. / Fu, M. / Silverman, R.B. / Petsko, G.A. / Ringe, D.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39214
Polymers43,7441
Non-polymers1,64713
Water7,386410
1
A: Aspartate aminotransferase
hetero molecules

A: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,78428
Polymers87,4892
Non-polymers3,29526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13680 Å2
ΔGint-119 kcal/mol
Surface area29130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.149, 84.760, 78.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second copy of the biological assembly is generated by the 2 fold axis: x, -y, -Z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aspartate aminotransferase / Transaminase A / ASPAT


Mass: 43744.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aspC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P00509, aspartate transaminase

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Non-polymers , 5 types, 423 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PSZ / 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]THIOPHENE-2-CARBOXYLIC ACID


Mass: 374.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15N2O7PS
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8
Details: 25 mM potassium phosphate, 43% saturated ammonium sulfate, 20 mM SADTA, pH 8.0, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→24.8 Å / Num. obs: 48869 / % possible obs: 98.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5143 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AMQ

1amq


Resolution: 1.75→24.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.349 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(I): 2.3 / ESU R: 0.145 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19031 2612 5.1 %RANDOM
Rwork0.14883 ---
obs0.15093 48869 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.359 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2--1.07 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 103 410 3590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223653
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9875020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67924.254181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02815631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6631529
X-RAY DIFFRACTIONr_chiral_restr0.1940.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022844
X-RAY DIFFRACTIONr_nbd_refined0.2240.21986
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2364
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.256
X-RAY DIFFRACTIONr_mcbond_it1.0521.52237
X-RAY DIFFRACTIONr_mcangle_it1.63923546
X-RAY DIFFRACTIONr_scbond_it2.62331596
X-RAY DIFFRACTIONr_scangle_it3.8344.51424
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 203 -
Rwork0.205 3597 -
obs--98.65 %

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