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- PDB-1k97: Crystal Structure of E. coli Argininosuccinate Synthetase in comp... -

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Basic information

Entry
Database: PDB / ID: 1k97
TitleCrystal Structure of E. coli Argininosuccinate Synthetase in complex with Aspartate and Citrulline
ComponentsARGININOSUCCINATE SYNTHASE
KeywordsLIGASE / N-TYPE ATP PYROPHOSPHATASE
Function / homology
Function and homology information


argininosuccinate synthase / argininosuccinate metabolic process / 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 / Argininosuccinate synthase, conserved site / Argininosuccinate synthase, type 1 subfamily / 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 / 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 / Helix Hairpins / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / CITRULLINE / Argininosuccinate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLemke, C.T. / Howell, P.L.
CitationJournal: 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
DepositionOct 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Aug 16, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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 3.0Nov 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 SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2763
Polymers50,9671
Non-polymers3082
Water5,963331
1
A: ARGININOSUCCINATE SYNTHASE
hetero molecules

A: ARGININOSUCCINATE SYNTHASE
hetero molecules

A: ARGININOSUCCINATE SYNTHASE
hetero molecules

A: ARGININOSUCCINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,10212
Polymers203,8694
Non-polymers1,2338
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 area31750 Å2
ΔGint-84 kcal/mol
Surface area54910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.996, 105.336, 127.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-575-

HOH

DetailsThe biological assembly is a tetramer from the monomer in the asymmetric unit by the operations: -X, -Y, Z and X, -Y, -Z and -X, Y, -Z

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Components

#1: Protein ARGININOSUCCINATE SYNTHASE / E.C.6.3.4.5 / CITRULLINE--ASPARTATE LIGASE / argininosuccinate synthetase /


Mass: 50967.262 Da / Num. of mol.: 1 / Fragment: Residues 1 to 444 / Mutation: C-term tag SVEHHHHHH
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-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 7.5 / Details: Lemke, C., (1999) Acta Crystallogr., 55, 2028.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 mMTris-HCl1droppH7.5
31.5-1.6 Mammonium sulfate1reservoir
4100 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→50 Å / Num. all: 35900 / Num. obs: 35667 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.7 Å2
Reflection shellResolution: 2→2.13 Å / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 97.6 % / Rmerge(I) obs: 0.265

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K91

1k91


Resolution: 2→20.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 810002.14 / 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
Rfree0.214 3479 10 %RANDOM
Rwork0.176 ---
obs0.176 34870 97.4 %-
all-35800 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1485 Å2 / ksol: 0.352627 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-6.65 Å20 Å20 Å2
2--2.17 Å20 Å2
3----8.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→20.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 21 331 3711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 581 10.4 %
Rwork0.207 5020 -
obs-5020 94.6 %
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
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.1757 / Rfactor Rfree: 0.2143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.386
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.078
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.874
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.259 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.207

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