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- PDB-1o17: ANTHRANILATE PHOSPHORIBOSYL-TRANSFERASE (TRPD) -

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Basic information

Entry
Database: PDB / ID: 1o17
TitleANTHRANILATE PHOSPHORIBOSYL-TRANSFERASE (TRPD)
ComponentsANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / nucleoside-phosphorylases
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
Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsMayans, O. / Ivens, A. / Kirschner, K. / Wilmanns, M.
Citation
Journal: Embo J. / Year: 2002
Title: Structural analysis of two enzymes catalysing reverse metabolic reactions implies common ancestry
Authors: Mayans, O. / Ivens, A. / Nissen, L. / Kirschner, K. / Wilmanns, M.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Purification, characterization and crystallization of thermostable anthranilate phosphoribosyltransferase from Sulfolobus solfataricus
Authors: Ivens, A. / Mayans, O. / Szadkowski, H. / Wilmanns, M. / Kirschner, K.
History
DepositionOct 29, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 1, 2002ID: 1K8E
Revision 1.0Nov 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
B: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
C: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
D: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)150,4784
Polymers150,4784
Non-polymers00
Water16,844935
1
A: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
D: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)75,2392
Polymers75,2392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-18 kcal/mol
Surface area26120 Å2
MethodPISA
2
B: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE
C: ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)75,2392
Polymers75,2392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-19 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.340, 65.850, 116.440
Angle α, β, γ (deg.)90.00, 107.56, 90.00
Int Tables number3
Cell settingmonoclinic
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11C-445-

HOH

Detailsbiological active form: dimer

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Components

#1: Protein
ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE / / E.C.2.4.2.18 / anthranilate PRT / trpD


Mass: 37619.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): KK8
References: UniProt: P50384, anthranilate phosphoribosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES pH7.0 or 0.05 M MES pH6.0 & 12-18% PEG 1500, VAPOR DIFFUSION, HANGING DROP at 293K, pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Details: Ivens, A., (2001) Eur.J.Biochem., 268, 2246.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16-8 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.0
312-18 %PEG15001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.834 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.834 Å / Relative weight: 1
ReflectionResolution: 2.05→18 Å / Num. obs: 77715 / % possible obs: 92.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.053 / Net I/σ(I): 10.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 3382 / Rsym value: 0.245 / % possible all: 81.2
Reflection
*PLUS
Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 81.2 % / Num. unique obs: 3382 / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→18 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 941 1.2 %random
Rwork0.213 ---
obs-77715 92.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-5.23 Å26.24 Å2
2--0 Å2-1.02 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10499 0 0 935 11434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.3881.5
X-RAY DIFFRACTIONc_mcangle_it2.2572
X-RAY DIFFRACTIONc_scbond_it2.2452
X-RAY DIFFRACTIONc_scangle_it3.3442.5
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4

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