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- PDB-1qdl: THE CRYSTAL STRUCTURE OF ANTHRANILATE SYNTHASE FROM SULFOLOBUS SO... -

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Basic information

Entry
Database: PDB / ID: 1qdl
TitleTHE CRYSTAL STRUCTURE OF ANTHRANILATE SYNTHASE FROM SULFOLOBUS SOLFATARICUS
Components
  • PROTEIN (ANTHRANILATE SYNTHASE (TRPE-SUBUNIT))
  • PROTEIN (ANTHRANILATE SYNTHASE (TRPG-SUBUNIT))
KeywordsLYASE / TRYPTOPHAN BIOSYNTHESIS / ANTHRANILATE SYNTHASE / GLUTAMINE AMIDOTRANSFERASE / ALLOSTERIC INTERACTION
Function / homology
Function and homology information


anthranilate synthase / anthranilate synthase activity / tryptophan biosynthetic process / glutamine metabolic process / metal ion binding
Similarity search - Function
Anthranilate synthase component I, archaeal type / 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, archaeal type / 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 / 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
Anthranilate synthase component 1 / Anthranilate synthase component 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKnoechel, T. / Ivens, A. / Hester, G. / Gonzalez, A. / Bauerle, R. / Wilmanns, M. / Kirschner, K. / Jansonius, J.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications.
Authors: Knochel, T. / Ivens, A. / Hester, G. / Gonzalez, A. / Bauerle, R. / Wilmanns, M. / Kirschner, K. / Jansonius, J.N.
#1: Journal: Thesis, University Basel / Year: 1998
Title: X-Ray Crystallographic Studies on Hyperthermostable Enzymes of the Tryptophan Biosynthesis Pathway: Three-Dimensional Structures of Indole-3-Glycerol Phosphate Synthase and Anthranilate Synthase
Authors: Knoechel, T.
History
DepositionMay 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ANTHRANILATE SYNTHASE (TRPE-SUBUNIT))
B: PROTEIN (ANTHRANILATE SYNTHASE (TRPG-SUBUNIT))


Theoretical massNumber of molelcules
Total (without water)69,7172
Polymers69,7172
Non-polymers00
Water2,342130
1
A: PROTEIN (ANTHRANILATE SYNTHASE (TRPE-SUBUNIT))
B: PROTEIN (ANTHRANILATE SYNTHASE (TRPG-SUBUNIT))

A: PROTEIN (ANTHRANILATE SYNTHASE (TRPE-SUBUNIT))
B: PROTEIN (ANTHRANILATE SYNTHASE (TRPG-SUBUNIT))


Theoretical massNumber of molelcules
Total (without water)139,4334
Polymers139,4334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)162.000, 162.000, 212.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein PROTEIN (ANTHRANILATE SYNTHASE (TRPE-SUBUNIT))


Mass: 47779.453 Da / Num. of mol.: 1 / Fragment: AMINODEOXYISOCHORISMATE SYNTHASE/LYASE SUBUNIT
Source method: isolated from a genetically manipulated source
Details: CONTAINS RESIDUES GLY-3,SER-2, HIS-1 PRIOR TO THE INITIATING METHIONINE
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q06128, anthranilate synthase
#2: Protein PROTEIN (ANTHRANILATE SYNTHASE (TRPG-SUBUNIT))


Mass: 21937.258 Da / Num. of mol.: 1 / Fragment: GLUTAMINE AMIDOTRANSFERASE SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q06129, anthranilate synthase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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

Crystal
*PLUS
Density % sol: 79 %
Crystal growpH: 7.5
Details: SODIUM CHLORIDE, PEG 6000, POTASSIUM PHOSPHATE, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mM1dropK2HPO4
31 mMEDTA1drop
40.4 mMdithiothreitol1drop
51.0-1.5 M1reservoirNaCl
62-5 %(w/v)PEG60001reservoir
7100 mM1reservoirK2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9095
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9095 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 57136 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.49
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.291 / % possible all: 99.6
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameClassification
MLPHAREphasing
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→30 Å / σ(F): 1
Details: A FLAT BULK-SOLVENT MODEL WAS SUPPLIED THROUGHOUT THE REFINEMENT. DIFFRACTION DATA WERE SUBJECTED TO AN OVERALL ANISOTROPIC B-FACTOR SCALING.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2887 -5%
Rwork0.226 ---
all0.228 ---
obs-57117 100 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4873 0 0 130 5003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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