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- PDB-1kp2: Crystal Structure of E. coli Argininosuccinate Synthetase in Comp... -

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Basic information

Entry
Database: PDB / ID: 1kp2
TitleCrystal Structure of E. coli Argininosuccinate Synthetase in Complex with ATP
Componentsargininosuccinate synthetase
KeywordsLIGASE / N-type ATP pyrophosphatase
Function / homology
Function and homology information


argininosuccinate metabolic process / argininosuccinate synthase / argininosuccinate synthase activity / urea cycle / L-arginine biosynthetic process / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / 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 / : ...Helix Hairpins - #400 / Argininosuccinate synthase, type 2 subfamily / Argininosuccinate synthetase mutimerisation domain, C-terminal tail / 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 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 / 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

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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)51,8186
Polymers50,9671
Non-polymers8515
Water5,152286
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)207,27424
Polymers203,8694
Non-polymers3,40520
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 area39350 Å2
ΔGint-207 kcal/mol
Surface area53780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.059, 104.050, 128.573
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-463-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -x,-y,z -x,y,-z x,-y,-z

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Components

#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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / 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-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.56 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium/postassium 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: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. all: 35733 / Num. obs: 34031 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.336 / % possible all: 86.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 45 Å / Num. obs: 35036 / % possible obs: 98 % / Num. measured all: 200378 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 86.6 % / Rmerge(I) obs: 0.38

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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→44.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 561488.12 / 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
Rfree0.216 3360 9.9 %RANDOM
Rwork0.177 ---
obs0.177 34031 95.2 %-
all-35733 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8462 Å2 / ksol: 0.377976 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.39 Å20 Å20 Å2
2---1.5 Å20 Å2
3----7.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 50 286 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 478 9.8 %
Rwork0.25 4406 -
obs--83.1 %
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_ASS.PARAMALL_ASS.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 45 Å / % reflection Rfree: 10 % / Rfactor obs: 0.1767 / Rfactor Rfree: 0.2164 / Rfactor Rwork: 0.1767
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.74
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.292 / Rfactor Rwork: 0.25

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