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- PDB-1i7s: ANTHRANILATE SYNTHASE FROM SERRATIA MARCESCENS IN COMPLEX WITH IT... -

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Basic information

Entry
Database: PDB / ID: 1i7s
TitleANTHRANILATE SYNTHASE FROM SERRATIA MARCESCENS IN COMPLEX WITH ITS END PRODUCT INHIBITOR L-TRYPTOPHAN
Components
  • ANTHRANILATE SYNTHASE
  • TRPG
KeywordsLYASE / ANTHRANILATE SYNTHASE / END PRODUCT INHIBITION / TRYPTOPHAN BINDING / CONFORMATIONAL CHANGE
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, 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 / 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 / Anthranilate synthase component 2
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSpraggon, G. / Kim, C. / Nguyen-Huu, X. / Yee, M.-C. / Yanofsky, C. / Mills, S.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product ...Title: The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan.
Authors: Spraggon, G. / Kim, C. / Nguyen-Huu, X. / Yee, M.C. / Yanofsky, C. / Mills, S.E.
History
DepositionMar 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ANTHRANILATE SYNTHASE
B: TRPG
C: ANTHRANILATE SYNTHASE
D: TRPG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6376
Polymers157,2294
Non-polymers4082
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-46 kcal/mol
Surface area48830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.271, 123.561, 179.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTHRANILATE SYNTHASE / / ANTHRANILATE SYNTHASE TRPE


Mass: 57664.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00897, anthranilate synthase
#2: Protein TRPG / ANTHRANILATE SYNTHASE TRPG


Mass: 20950.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00900, anthranilate synthase
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2

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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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growpH: 5.4 / Details: pH 5.40
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
215 %(v/v)glycerol1drop
32 mMdithiothreitol1drop
410 mMEDTA1drop
525 mg/mlprotein1drop
625 %PEG60001reservoir
7100 mMcitrate1reservoir
8100 mMglutamate1reservoir
934.5 mMglutamine1reservoir
108 mM1reservoirMgCl2
110.5 mMtryptophan1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→44.91 Å / % possible obs: 93.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 44.91 Å / Num. obs: 59826 / Redundancy: 5.4 % / Biso Wilson estimate: 54.3 Å2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.0 REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1QDL

1qdl


Resolution: 2.4→44.9 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.318 3024 5.1 %RANDOM R VALUE (WORKING + TEST SET) : 0.247
Rwork0.247 ---
obs0.247 59488 --
Displacement parametersBiso mean: 60.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2--1.57 Å20 Å2
3----3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10850 0 30 0 10880
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.08
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg25.19
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.35
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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