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- PDB-3pa9: Mechanism of inactivation of E. coli aspartate aminotransferase b... -

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Basic information

Entry
Database: PDB / ID: 3pa9
TitleMechanism of inactivation of E. coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) pH 7.5
ComponentsAspartate aminotransferaseAspartate transaminase
KeywordsTRANSFERASE / PLP / PMP / SADFA / catalytic lysine
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / amino acid metabolic process / transaminase activity / biosynthetic process / pyridoxal phosphate binding
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-aminofuran-2-carboxylic acid / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLiu, D. / Pozharski, E. / Fu, M. / Silverman, R.B. / Ringe, D.
CitationJournal: Biochemistry / Year: 2010
Title: Mechanism of inactivation of Escherichia coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid .
Authors: Liu, D. / Pozharski, E. / Fu, M. / Silverman, R.B. / Ringe, D.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 6, 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_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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)45,39218
Polymers43,6191
Non-polymers1,77317
Water7,566420
1
A: Aspartate aminotransferase
hetero molecules

A: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,78436
Polymers87,2382
Non-polymers3,54534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area14210 Å2
ΔGint-122 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.135, 85.532, 79.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Aspartate aminotransferase / Aspartate transaminase


Mass: 43619.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: D3H0F7, aspartate transaminase

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Non-polymers , 5 types, 437 molecules

#2: Chemical ChemComp-PJ7 / 4-aminofuran-2-carboxylic acid


Mass: 127.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5NO3
#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE STARTING INACTIVATOR MOLECULE (S)-4-AMINO-4,5-DYHIDRO-2-FURANCARBOXYLIC ACID (S-ADFA) UNDERGOES ...THE STARTING INACTIVATOR MOLECULE (S)-4-AMINO-4,5-DYHIDRO-2-FURANCARBOXYLIC ACID (S-ADFA) UNDERGOES A CHEMICAL TRANSFORMATION BY IRREVERSIBLY BINDING TO THE ACTIVE SITE RESIDUE K246 OF ASPC. THE LIGAND PJ7 REPRESENTS FINAL PRODUCT

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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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7.5
Details: Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→77.2 Å / Num. obs: 67102 / % possible obs: 97.7 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMQ

1amq


Resolution: 1.7→77.15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.485 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18519 2851 5.1 %RANDOM
Rwork0.14827 ---
obs0.15012 53395 97.83 %-
all-67102 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.043 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.55 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→77.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 110 420 3599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223580
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9894898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1424.253174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48415612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3141528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022755
X-RAY DIFFRACTIONr_nbd_refined0.220.21852
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2380
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.243
X-RAY DIFFRACTIONr_mcbond_it0.9741.52186
X-RAY DIFFRACTIONr_mcangle_it1.54323474
X-RAY DIFFRACTIONr_scbond_it2.44531543
X-RAY DIFFRACTIONr_scangle_it3.5524.51381
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 206 -
Rwork0.195 3775 -
obs--94.43 %

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