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- PDB-1c3u: T. MARITIMA ADENYLOSUCCINATE LYASE -

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Basic information

Entry
Database: PDB / ID: 1c3u
TitleT. MARITIMA ADENYLOSUCCINATE LYASE
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-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsToth, E.A. / Yeates, T.O.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: The structure of adenylosuccinate lyase, an enzyme with dual activity in the de novo purine biosynthetic pathway.
Authors: Toth, E.A. / Yeates, T.O.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: ADENYLOSUCCINATE LYASE
B: ADENYLOSUCCINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2816
Polymers99,8962
Non-polymers3844
Water7,062392
1
A: ADENYLOSUCCINATE LYASE
B: ADENYLOSUCCINATE LYASE
hetero molecules

A: ADENYLOSUCCINATE LYASE
B: ADENYLOSUCCINATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,56112
Polymers199,7934
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area26880 Å2
ΔGint-236 kcal/mol
Surface area56350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.498, 126.213, 169.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ADENYLOSUCCINATE LYASE


Mass: 49948.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0I0, adenylosuccinate lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 392 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Bicine, 5 mM AMP, 1.8 M Ammonium Sulfate, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
30.1-0.5 %PEG40001reservoir
46 %(v/v)glycerol1reservoir
51 mMbeta-mercaptoethanol1reservoir
60.02 %(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 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.3→87.04 Å / Num. obs: 57257 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 21.46 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 22.67
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.263 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.263

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Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.3→50 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2902 -RANDOM
Rwork0.199 ---
obs-57257 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6716 0 20 392 7128
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.84

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