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- PDB-1f1o: STRUCTURAL STUDIES OF ADENYLOSUCCINATE LYASES -

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Basic information

Entry
Database: PDB / ID: 1f1o
TitleSTRUCTURAL STUDIES OF ADENYLOSUCCINATE LYASES
ComponentsADENYLOSUCCINATE LYASE
KeywordsLYASE / purine biosynthesis
Function / homology
Function and homology information


AMP biosynthetic process / adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / cytosol
Similarity search - Function
Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
Adenylosuccinate lyase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.25 Å
AuthorsToth, E.A. / Yeates, T.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds.
Authors: Toth, E.A. / Worby, C. / Dixon, J.E. / Goedken, E.R. / Marqusee, S. / Yeates, T.O.
History
DepositionMay 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 99The coordinate section in this entry contains CA atoms only

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENYLOSUCCINATE LYASE


Theoretical massNumber of molelcules
Total (without water)49,5541
Polymers49,5541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.530, 129.530, 282.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ADENYLOSUCCINATE LYASE / / ASL / Coordinate model: Cα atoms only


Mass: 49553.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P12047, adenylosuccinate lyase

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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: 6.89 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1 M MES, 1.5 M ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 47.7 %
Crystal grow
*PLUS
Temperature: 18 ℃
Details: This particular structure is not described in this paper.
pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Mcitric acid1reservoirpH5.0
210-20 %(w/v)PEG40001reservoir
30.02 %(w/v)1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 22850 / Num. obs: 2843 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.058
Reflection
*PLUS
Num. measured all: 22850

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3.25→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.355 962 random
Rwork0.336 --
all-22850 -
obs-19909 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.494 Å2-2.949 Å20 Å2
2--0.494 Å20 Å2
3----0.989 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms351 0 0 0 351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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