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- PDB-1jsw: NATIVE L-ASPARTATE AMMONIA LYASE -

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Basic information

Entry
Database: PDB / ID: 1jsw
TitleNATIVE L-ASPARTATE AMMONIA LYASE
ComponentsL-ASPARTATE AMMONIA-LYASE
KeywordsAMINO ACID AMMONIA-LYASE
Function / homology
Function and homology information


aspartate ammonia-lyase / aspartate ammonia-lyase activity / aspartate metabolic process / tricarboxylic acid cycle / membrane / cytosol
Similarity search - Function
Aspartate ammonia-lyase / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Aspartate ammonia-lyase / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / beta-D-glucopyranose / Aspartate ammonia-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsShi, W. / Dunbar, J. / Farber, G.K.
Citation
Journal: Biochemistry / Year: 1997
Title: The structure of L-aspartate ammonia-lyase from Escherichia coli.
Authors: Shi, W. / Dunbar, J. / Jayasekera, M.M. / Viola, R.E. / Farber, G.K.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Studies of L-Aspartase from Escherichia Coli
Authors: Shi, W. / Kidd, R. / Giorgianni, F. / Schindler, J.F. / Viola, R.E. / Farber, G.K.
History
DepositionFeb 19, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ASPARTATE AMMONIA-LYASE
B: L-ASPARTATE AMMONIA-LYASE
C: L-ASPARTATE AMMONIA-LYASE
D: L-ASPARTATE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,0477
Polymers209,6284
Non-polymers4193
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27350 Å2
ΔGint-143 kcal/mol
Surface area57060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.500, 146.200, 103.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
L-ASPARTATE AMMONIA-LYASE / L-ASPARTASE


Mass: 52406.883 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: B / References: UniProt: P0AC38, aspartate ammonia-lyase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.77 Å3/Da / Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-13 mg/mlprotein11
250 mMTris-HEPES11
30.1 MTris-HCl12
426 %PEG335012
50.30 Msodium acetate12
64 mMdithiothreitol12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 26, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 57964 / % possible obs: 80.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 156675

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.7→10 Å / σ(F): 2
Details: RESIDUE 32 WAS MODELED AS A VAL FOR MOST OF THE REFINEMENT CYCLES BECAUSE OF CONFLICTING SEQUENCES AT THIS POSITION. A SEQUENCING GEL CONFIRMED THAT THIS RESIDUE IS ACTUALLY GLU. THE RESIDUE ...Details: RESIDUE 32 WAS MODELED AS A VAL FOR MOST OF THE REFINEMENT CYCLES BECAUSE OF CONFLICTING SEQUENCES AT THIS POSITION. A SEQUENCING GEL CONFIRMED THAT THIS RESIDUE IS ACTUALLY GLU. THE RESIDUE WAS CHANGED TO GLU FOR THE FINAL REFINEMENT CYCLE.
RfactorNum. reflection% reflection
Rfree0.371 -10 %
Rwork0.216 --
obs0.216 43803 -
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13667 0 28 69 13764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.371 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51

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