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

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Basic information

Entry
Database: PDB / ID: 3paa
TitleMechanism of inactivation of E. coli aspartate aminotransferase by (S)-4-amino-4,5-dihydro-2-furancarboxylic acid (S-ADFA) pH 8.0
ComponentsAspartate aminotransferaseAspartate transaminase
KeywordsTRANSFERASE / PMP / SADFA
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: 1.9 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 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water7,602422
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 area14150 Å2
ΔGint-117 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.846, 85.769, 79.005
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) / Gene: aspC / Production host: Escherichia coli (E. coli) / References: UniProt: D3H0F7, aspartate transaminase

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Non-polymers , 5 types, 439 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.: 422 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 297 K / pH: 8
Details: Ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.97
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: 1.9→77.3 Å / Num. obs: 49045 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
Blu-Iceicedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→77.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.179 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2114 5.1 %RANDOM
Rwork0.137 ---
obs0.139 39722 99.9 %-
all-49045 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--1 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→77.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 110 422 3601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223544
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9894832
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59124.244172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8261527
X-RAY DIFFRACTIONr_chiral_restr0.0940.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022704
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21847
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2403
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0491.52167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61623422
X-RAY DIFFRACTIONr_scbond_it2.64431538
X-RAY DIFFRACTIONr_scangle_it3.8834.51374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 174 -
Rwork0.166 2905 -
obs--99.81 %

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