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- PDB-1c3c: T. MARITIMA ADENYLOSUCCINATE LYASE -

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Basic information

Entry
Database: PDB / ID: 1c3c
TitleT. MARITIMA ADENYLOSUCCINATE LYASE
ComponentsPROTEIN (ADENYLOSUCCINATE 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 / 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
: / Adenylosuccinate lyase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ADENYLOSUCCINATE LYASE)
B: PROTEIN (ADENYLOSUCCINATE LYASE)


Theoretical massNumber of molelcules
Total (without water)99,3762
Polymers99,3762
Non-polymers00
Water12,484693
1
A: PROTEIN (ADENYLOSUCCINATE LYASE)
B: PROTEIN (ADENYLOSUCCINATE LYASE)

A: PROTEIN (ADENYLOSUCCINATE LYASE)
B: PROTEIN (ADENYLOSUCCINATE LYASE)


Theoretical massNumber of molelcules
Total (without water)198,7514
Polymers198,7514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area25880 Å2
ΔGint-106 kcal/mol
Surface area56350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.809, 126.753, 169.000
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 PROTEIN (ADENYLOSUCCINATE LYASE)


Mass: 49687.832 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, GenBank: 4981640, adenylosuccinate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growpH: 4.5
Details: 100 MM NAACETATE, 0.5% PEG 4000, 6% GLYCEROL, pH 4.50
Crystal grow
*PLUS
Temperature: 18 ℃ / 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: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.4 Å / Num. obs: 117163 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.33 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.67
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.1 / % possible all: 84.1
Reflection shell
*PLUS
% possible obs: 84.1 %

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→50 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5858 5 %RANDOM
Rwork0.179 ---
obs-117163 97.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6734 0 0 693 7427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d2.64
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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