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- PDB-2pts: Crystal structure of wild type Escherichia coli adenylosuccinate lyase -

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Basic information

Entry
Database: PDB / ID: 2pts
TitleCrystal structure of wild type Escherichia coli adenylosuccinate lyase
ComponentsAdenylosuccinate lyase
KeywordsLYASE / adenylosuccinate lyase / wild-type-selenomethionine substituted
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 / guanosine tetraphosphate binding / DNA damage response / cytosol
Similarity search - Function
: / Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...: / Adenylosuccinate lyase PurB, C-terminal / Adenylosuccinate lyase C-terminal / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTsai, M. / Howell, P.L.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism.
Authors: Tsai, M. / Koo, J. / Yip, P. / Colman, R.F. / Segall, M.L. / Howell, P.L.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model

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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)52,8591
Polymers52,8591
Non-polymers00
Water8,233457
1
A: Adenylosuccinate lyase

A: Adenylosuccinate lyase

A: Adenylosuccinate lyase

A: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)211,4344
Polymers211,4344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area27250 Å2
ΔGint-135 kcal/mol
Surface area58500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.374, 98.406, 136.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-707-

HOH

21A-879-

HOH

DetailsThe biological assembly is a homotetramer generated from the monomer in the asymmetric unit by the operations: (-x, -y, z; x, -y, -z; -x, y, -z).

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Components

#1: Protein Adenylosuccinate lyase / / Adenylosuccinate / ASL


Mass: 52858.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: purB / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P0AB89, adenylosuccinate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, sodium acetate tri-hydrate, PEG-4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 60020 / Num. obs: 59885 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 7.4 Å2 / Rsym value: 4.8 / Net I/σ(I): 88.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 58.8 / Rsym value: 7.6 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2932 -random
Rwork0.165 ---
all-60020 --
obs-59885 99.8 %-
Displacement parametersBiso mean: 14.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å2--
2---1.84 Å2-
3---0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 0 457 3971
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d19.6
X-RAY DIFFRACTIONx_improper_angle_d0.71
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.211 358 -
Rwork0.158 --
obs-7452 99.5 %

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