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- PDB-1dof: THE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM ... -

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Basic information

Entry
Database: PDB / ID: 1dof
TitleTHE CRYSTAL STRUCTURE OF ADENYLOSUCCINATE LYASE FROM PYROBACULUM AEROPHILUM: INSIGHTS INTO THERMAL STABILITY AND HUMAN PATHOLOGY
ComponentsADENYLOSUCCINATE LYASE
KeywordsLYASE / purine biosynthesis
Function / homology
Function and homology information


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-terminal domain / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...: / Adenylosuccinate Lyase, C-terminal domain / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / 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
Adenylosuccinate lyase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsToth, E.A. / Yeates, T.O. / Goedken, E. / Dixon, J.E. / Marqusee, S.
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
DepositionDec 20, 1999Deposition 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: ADENYLOSUCCINATE LYASE
B: ADENYLOSUCCINATE LYASE
C: ADENYLOSUCCINATE LYASE
D: ADENYLOSUCCINATE LYASE


Theoretical massNumber of molelcules
Total (without water)181,6934
Polymers181,6934
Non-polymers00
Water14,268792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28420 Å2
ΔGint-131 kcal/mol
Surface area43870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.620, 150.310, 173.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ADENYLOSUCCINATE LYASE


Mass: 45423.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZY28, adenylosuccinate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Citric Acid, 10-20% PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 47.7 %
Crystal grow
*PLUS
Temperature: 18 ℃
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: X8C / Wavelength: 0.908
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.1→48.05 Å / Num. all: 100910 / Num. obs: 100737 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.302 / % possible all: 98.8
Reflection
*PLUS
Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.1→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 5017 random
Rwork0.203 --
all-100552 -
obs-100508 -
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11872 0 0 792 12664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_deg2.98
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS

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