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- PDB-1kh2: Crystal Structure of Thermus thermophilus HB8 Argininosuccinate S... -

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Basic information

Entry
Database: PDB / ID: 1kh2
TitleCrystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with ATP
ComponentsArgininosuccinate Synthetase
KeywordsLIGASE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate metabolic process / argininosuccinate synthase activity / urea cycle / L-arginine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase / Argininosuccinate synthase, conserved site / Argininosuccinate synthase, type 1 subfamily / 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 / Argininosuccinate synthase, conserved site / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthetase, catalytic/multimerisation domain body / : / : / Arginosuccinate synthase N-terminal HUP domain / Arginosuccinate synthase C-terminal 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-5'-TRIPHOSPHATE / Argininosuccinate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGoto, M. / Nakajima, Y. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action.
Authors: Goto, M. / Nakajima, Y. / Hirotsu, K.
History
DepositionNov 29, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Apr 8, 2020Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_validate_close_contact / struct_conn
Revision 1.5Mar 13, 2024Group: 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

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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)181,5338
Polymers179,5044
Non-polymers2,0294
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28740 Å2
ΔGint-136 kcal/mol
Surface area50430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.91, 228.91, 161.68
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


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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 4.54 Å3/Da / Density % sol: 72.9 %
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
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
22.4 Mammonium sulfate1reservoir
330 %(v/v)glycerol1reservoir
4100 mMTris-HCl1reservoirpH8.5
510 mMATP1reservoir
610 mM1reservoirMgCl2

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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: Sep 22, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.96 Å / Num. all: 143708 / Num. obs: 143708 / % possible obs: 99.9 %
Reflection shellResolution: 2.3→2.37 Å / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 685640 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.27

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.241 13831 9.985 %
Rwork0.209 --
all-143708 -
obs-138518 -
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12172 0 124 385 12681
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.431
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 19.9 Å / Rfactor obs: 0.2087 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.2087
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.43
LS refinement shell
*PLUS
Rfactor Rfree: 0.3149 / Rfactor Rwork: 0.2676 / Rfactor obs: 0.2676

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