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- PDB-1i1q: STRUCTURE OF THE COOPERATIVE ALLOSTERIC ANTHRANILATE SYNTHASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1i1q
TitleSTRUCTURE OF THE COOPERATIVE ALLOSTERIC ANTHRANILATE SYNTHASE FROM SALMONELLA TYPHIMURIUM
Components
  • ANTHRANILATE SYNTHASE COMPONENT I
  • ANTHRANILATE SYNTHASE COMPONENT II
KeywordsLYASE / Tryptophan biosynthesis
Function / homology
Function and homology information


anthranilate synthase / anthranilate synthase activity / phenazine biosynthetic process / anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / glutamine metabolic process / magnesium ion binding / metal ion binding
Similarity search - Function
Anthranilate synthase component I, TrpE-like, bacterial / Anthranilate synthase/para-aminobenzoate synthase like domain / Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme ...Anthranilate synthase component I, TrpE-like, bacterial / Anthranilate synthase/para-aminobenzoate synthase like domain / Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / Anthranilate phosphoribosyl transferase / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Anthranilate synthase component 1 / Bifunctional protein TrpGD
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 1.9 Å
AuthorsMorollo, A.A. / Eck, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the cooperative allosteric anthranilate synthase from Salmonella typhimurium.
Authors: Morollo, A.A. / Eck, M.J.
History
DepositionFeb 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The transformations generate the active heterotetramer.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTHRANILATE SYNTHASE COMPONENT I
B: ANTHRANILATE SYNTHASE COMPONENT II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1103
Polymers77,9062
Non-polymers2041
Water2,270126
1
A: ANTHRANILATE SYNTHASE COMPONENT I
B: ANTHRANILATE SYNTHASE COMPONENT II
hetero molecules

A: ANTHRANILATE SYNTHASE COMPONENT I
B: ANTHRANILATE SYNTHASE COMPONENT II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,2206
Polymers155,8124
Non-polymers4082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-15 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.000, 101.700, 67.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ANTHRANILATE SYNTHASE COMPONENT I /


Mass: 57150.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSTS23 / Production host: Escherichia coli (E. coli) / References: UniProt: P00898, anthranilate synthase
#2: Protein ANTHRANILATE SYNTHASE COMPONENT II /


Mass: 20754.855 Da / Num. of mol.: 1 / Fragment: GLUTAMINE AMIDOTRANSFERASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSTS23 / Production host: Escherichia coli (E. coli) / References: UniProt: P00905, anthranilate synthase
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 49 % / Description: SEE NAT.STRUCT.BIOL. 8, 243-247.
Crystal growpH: 7.5 / Details: Potassium phosphate, PEG 8000, EDTA, DTT, pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
22 mMdithiothreitol1drop
350 mM1reservoirKH2PO4
410-20 %(w/v)PEG80001reservoir
50.1 mMEDTA1reservoir
62 mMdithiothreitol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONCHESS F110.9220, 1.5418
ROTATING ANODERIGAKU RU3002
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9221
21.54181
ReflectionResolution: 1.9→25 Å / Num. obs: 64243 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 26.45
Reflection shellResolution: 1.9→1.98 Å / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 2.59 / % possible all: 62.8
Reflection shell
*PLUS
% possible obs: 62.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: SELENOMETHIONYL TRPE SOLVED BY MAD

Resolution: 1.9→24.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2407998.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3060 5.1 %RANDOM
Rwork0.219 ---
obs0.219 60248 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.91 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.34 Å20 Å20 Å2
2---2.76 Å20 Å2
3---10.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5349 0 15 126 5490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 425 5.3 %
Rwork0.291 7639 -
obs--77 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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