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- PDB-1j20: Crystal Structure of Thermus thermophilus HB8 Argininosuccinate S... -

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Basic information

Entry
Database: PDB / ID: 1j20
TitleCrystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with product
ComponentsArgininosuccinate SynthetaseArgininosuccinate synthase
KeywordsLIGASE / ATP-binding / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate synthase activity / arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
: / : / Arginosuccinate synthase C-terminal domain / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain ...: / : / Arginosuccinate synthase C-terminal domain / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthetase, catalytic/multimerisation domain body / Arginosuccinate synthase N-terminal HUP domain / Argininosuccinate synthase signature 1. / Argininosuccinate synthase signature 2. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ARGININOSUCCINATE / Argininosuccinate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGoto, M. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structures of argininosuccinate synthetase in enzyme-ATP-substrates and enzyme-AMP-product forms
Authors: Goto, M. / Omi, R. / Miyahara, I. / Sugahara, M. / Hirotsu, K.
History
DepositionDec 24, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Argininosuccinate Synthetase
B: Argininosuccinate Synthetase
C: Argininosuccinate Synthetase
D: Argininosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,43816
Polymers179,5044
Non-polymers2,93412
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33060 Å2
ΔGint-200 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.78, 228.78, 159.41
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Argininosuccinate Synthetase / Argininosuccinate synthase


Mass: 44875.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P59846, argininosuccinate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-AS1 / ARGININOSUCCINATE / Argininosuccinic acid


Mass: 290.273 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18N4O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 4.31 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: tris, ammonium sulfate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
22.4 Mammonium sulfate1reservoir
330 %(v/v)glycerol1reservoir
4100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 209661 / Num. obs: 209661 / % possible obs: 99.4 %
Reflection shellResolution: 2→2.07 Å / % possible all: 99
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. measured all: 670809 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.239 20568 RANDOM
Rwork0.212 --
all-209661 -
obs-206687 -
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12264 0 192 862 13318
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.609
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.2189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.61
LS refinement shell
*PLUS
Rfactor Rfree: 0.3051 / Rfactor Rwork: 0.2811

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