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- PDB-2gvq: Anthranilate phosphoribosyl-transferase (TRPD) from S. solfataric... -

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Basic information

Entry
Database: PDB / ID: 2gvq
TitleAnthranilate phosphoribosyl-transferase (TRPD) from S. solfataricus in complex with anthranilate
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / PROTEIN-LIGAND COMPLEX
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / 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 ...Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / 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 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-AMINOBENZOIC ACID / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.43 Å
AuthorsMarino, M. / Deuss, M. / Sterner, R. / Mayans, O.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and mutational analysis of substrate complexation by anthranilate phosphoribosyltransferase from Sulfolobus solfataricus.
Authors: Marino, M. / Deuss, M. / Svergun, D.I. / Konarev, P.V. / Sterner, R. / Mayans, O.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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
Revision 2.0Nov 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: Anthranilate phosphoribosyltransferase
B: Anthranilate phosphoribosyltransferase
C: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,43811
Polymers150,4784
Non-polymers9607
Water4,558253
1
A: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6505
Polymers75,2392
Non-polymers4113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-3 kcal/mol
Surface area25570 Å2
MethodPISA
2
B: Anthranilate phosphoribosyltransferase
C: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7886
Polymers75,2392
Non-polymers5494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint4 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.814, 65.621, 115.607
Angle α, β, γ (deg.)90.00, 107.39, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11D-610-

HOH

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Components

#1: Protein
Anthranilate phosphoribosyltransferase / TRPD


Mass: 37619.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: TRPD / Plasmid: pQE40 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 trpEA2
References: UniProt: P50384, anthranilate phosphoribosyltransferase
#2: Chemical
ChemComp-BE2 / 2-AMINOBENZOIC ACID


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.4 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1500, MES, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.951 / Wavelength: 0.951 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 11, 2002
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 2.43→20 Å / Num. obs: 49363 / % possible obs: 97.9 % / Redundancy: 3.84 % / Rsym value: 0.065 / Net I/σ(I): 10.99
Reflection shellResolution: 2.43→2.5 Å / Redundancy: 3.41 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.43 / % possible all: 96.2

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1O17

1o17


Resolution: 2.43→20 Å / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.242 584 RANDOM
Rwork0.199 --
obs-49363 -
Displacement parametersBiso mean: 42.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.629 Å20 Å2-0.464 Å2
2--9.432 Å20 Å2
3----8.804 Å2
Refinement stepCycle: LAST / Resolution: 2.43→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10503 0 70 253 10826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33

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