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- PDB-2d7u: Crystal structure of hypothetical adenylosuccinate synthetase, PH... -

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Basic information

Entry
Database: PDB / ID: 2d7u
TitleCrystal structure of hypothetical adenylosuccinate synthetase, PH0438 from Pyrococcus horikoshii OT3
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / Structural Genomics / conserved hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Adenylosuccinate synthetase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXie, Y. / Kishisita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of hypothetical adenylosuccinate synthetase, PH0438 from Pyrococcus horikoshii OT3
Authors: Xie, Y. / Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionNov 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)37,2801
Polymers37,2801
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Adenylosuccinate synthetase

A: Adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)74,5612
Polymers74,5612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+2/31
Buried area4010 Å2
ΔGint-21 kcal/mol
Surface area23560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.200, 57.200, 170.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
DetailsIn this crystal packing, it looks like monomer. But, there is no experimental evidence.

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Components

#1: Protein Adenylosuccinate synthetase / IMP--aspartate ligase / AdSS / AMPSase


Mass: 37280.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58187, adenylosuccinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 43.23 %
Crystal growTemperature: 291 K / Method: oil batch / pH: 8.7
Details: 13.5% PEG 20000, 0.1M Tris-HCl, pH 8.7, OIL BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Aug 27, 2005 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 11717 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 34.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 38.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 767 / Rsym value: 0.184 / % possible all: 64.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SOO

1soo


Resolution: 2.5→47.58 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 770420.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 576 5.1 %RANDOM
Rwork0.236 ---
obs0.236 11262 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9739 Å2 / ksol: 0.368351 e/Å3
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.14 Å25.8 Å20 Å2
2--4.14 Å20 Å2
3----8.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 0 106 2592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.57
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 72 4 %
Rwork0.297 1750 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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