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- PDB-1yis: Structural genomics of Caenorhabditis elegans: adenylosuccinate lyase -

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Basic information

Entry
Database: PDB / ID: 1yis
TitleStructural genomics of Caenorhabditis elegans: adenylosuccinate lyase
Componentsadenylosuccinate lyase
KeywordsLYASE / Caenorhabditis / X-ray structure / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / 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 / Adenylosuccinate lyase C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 ...Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / 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 speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSymersky, J. / Schormann, N. / Lu, S. / Zhang, Y. / Karpova, E. / Qiu, S. / Huang, W. / Cao, Z. / Zhou, J. / Luo, M. ...Symersky, J. / Schormann, N. / Lu, S. / Zhang, Y. / Karpova, E. / Qiu, S. / Huang, W. / Cao, Z. / Zhou, J. / Luo, M. / Arabshahi, A. / McKinstry, A. / Luan, C.-H. / Luo, D. / Johnson, D. / An, J. / Tsao, J. / Delucas, L. / Shang, Q. / Gray, R. / Li, S. / Bray, T. / Chen, Y.-J. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Structural genomics of Caenorhabditis elegans: adenylosuccinate lyase
Authors: Symersky, J. / Schormann, N. / Lu, S. / Zhang, Y. / Karpova, E. / Qiu, S. / Huang, W. / Cao, Z. / Zhou, J. / Luo, M. / Arabshahi, A. / McKinstry, A. / Luan, C.-H. / Luo, D. / Johnson, D. / ...Authors: Symersky, J. / Schormann, N. / Lu, S. / Zhang, Y. / Karpova, E. / Qiu, S. / Huang, W. / Cao, Z. / Zhou, J. / Luo, M. / Arabshahi, A. / McKinstry, A. / Luan, C.-H. / Luo, D. / Johnson, D. / An, J. / Tsao, J. / Delucas, L. / Shang, Q. / Gray, R. / Li, S. / Bray, T. / Chen, Y.-J.
History
DepositionJan 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2962
Polymers54,2001
Non-polymers961
Water4,107228
1
A: adenylosuccinate lyase
hetero molecules

A: adenylosuccinate lyase
hetero molecules

A: adenylosuccinate lyase
hetero molecules

A: adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,1858
Polymers216,8014
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
Buried area25740 Å2
ΔGint-148 kcal/mol
Surface area57500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.242, 124.242, 165.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Cell settingtetragonal
Space group name H-MI422

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Components

#1: Protein adenylosuccinate lyase / / E.C.4.3.2.2 / fumarate lyase (53.6 kD) (1H824)


Mass: 54200.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: Q21774, adenylosuccinate lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.49 M AMMONIUM SULFATE, 0.1 M CITRIC ACID, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 48535 / Num. obs: 48307 / % possible obs: 100 % / Observed criterion σ(I): -1 / Redundancy: 7.7 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4846 / Rsym value: 0.215 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 4420 9.2 %random
Rwork0.174 ---
all-48535 --
obs-48307 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4013 Å2 / ksol: 0.39258 e/Å3
Displacement parametersBiso mean: 27.16 Å2
Baniso -1Baniso -2Baniso -3
1--3.552 Å20 Å20 Å2
2---3.552 Å20 Å2
3---7.105 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 5 228 3551
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.1911.5
X-RAY DIFFRACTIONc_mcangle_it1.8992
X-RAY DIFFRACTIONc_scbond_it2.4292
X-RAY DIFFRACTIONc_scangle_it3.3992.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 456 5.7 %
Rwork0.195 7584 -
obs-8040 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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