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- PDB-1kp3: Crystal Structure of E. coli Argininosuccinate Synthetase in Comp... -

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Basic information

Entry
Database: PDB / ID: 1kp3
TitleCrystal Structure of E. coli Argininosuccinate Synthetase in Complex with ATP and Citrulline
Componentsargininosuccinate synthetase
KeywordsLIGASE / N-Type ATP pyrophosphatase
Function / homology
Function and homology information


argininosuccinate metabolic process / argininosuccinate synthase / argininosuccinate synthase activity / urea cycle / arginine biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / : / : / Arginosuccinate synthase C-terminal domain / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthetase, chain A, domain 2 / Argininosuccinate synthase, type 1 subfamily / Argininosuccinate synthase ...Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / : / : / 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 / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CITRULLINE / GUANIDINE / PHOSPHATE ION / Argininosuccinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLemke, C.T. / Howell, P.L.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Substrate Induced Conformational Changes in Argininosuccinate Synthetase
Authors: Lemke, C.T. / Howell, P.L.
#1: Journal: Structure / Year: 2001
Title: The 1.6 A Crystal Structure of E. coli Argininosuccinate Synthetase Suggests a Conformational Change during Catalysis
Authors: Lemke, C.T. / Howell, P.L.
History
DepositionDec 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: argininosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0387
Polymers50,9671
Non-polymers1,0716
Water3,351186
1
A: argininosuccinate synthetase
hetero molecules

A: argininosuccinate synthetase
hetero molecules

A: argininosuccinate synthetase
hetero molecules

A: argininosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,15228
Polymers203,8694
Non-polymers4,28324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area44000 Å2
ΔGint-85 kcal/mol
Surface area50220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.478, 104.222, 128.835
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-468-

HOH

21A-550-

HOH

31A-600-

HOH

DetailsThe biological assembly is a tetramer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein argininosuccinate synthetase


Mass: 50967.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARGG / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / References: UniProt: P0A6E4, argininosuccinate synthase

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13N3O3
#5: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.52 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium/potassium phosphate, guanidine hydrochloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
225 mMMES1droppH6.5
35 mMATP1drop
415 mM1dropMgCl2
5150 mMguanidine hydrochloride1drop
62.0 Msodium potassium phosphate1drop
7100 mMMES1droppH6.5
81.6 Msodium potassium phosphate1reservoir
9100 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→41 Å / Num. all: 35158 / Num. obs: 32696 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 11.8
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.396 / % possible all: 71.9
Reflection
*PLUS
Highest resolution: 1.99 Å / Lowest resolution: 41 Å / Num. obs: 34170 / % possible obs: 95.6 % / Num. measured all: 229900 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 71.9 % / Rmerge(I) obs: 0.396

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K92

1k92


Resolution: 2→40.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 452054.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3272 10 %RANDOM
Rwork0.192 ---
obs0.192 32696 92.9 %-
all-35158 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.3294 Å2 / ksol: 0.407088 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1-14.11 Å20 Å20 Å2
2---5.17 Å20 Å2
3----8.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 68 186 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 422 9.7 %
Rwork0.283 3917 -
obs--74.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ALL_AS.PARAMALL_AS.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 41 Å / % reflection Rfree: 10 % / Rfactor obs: 0.1916 / Rfactor Rfree: 0.2294 / Rfactor Rwork: 0.1916
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.91
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / Rfactor Rwork: 0.283

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