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- PDB-7dsj: Anthranilate phosphoribosyltransferase from Saccharomyces cerevis... -

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Basic information

Entry
Database: PDB / ID: 7dsj
TitleAnthranilate phosphoribosyltransferase from Saccharomyces cerevisiae in complex with PRPP and Mg
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Tryptophan biosynthesis
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / L-tryptophan biosynthetic process / nucleus / cytosol / cytoplasm
Similarity search - Function
Anthranilate phosphoribosyl transferase / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PRP / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsWu, X.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0504903 China
National Natural Science Foundation of China (NSFC)31621002 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae.
Authors: Wu, X. / Zhang, M. / Kuang, Z. / Yue, J. / Xue, L. / Zhu, M. / Zhu, Z. / Khan, M.H. / Niu, L.
History
DepositionDec 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthranilate phosphoribosyltransferase
B: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2326
Polymers83,4032
Non-polymers8294
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-62 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.328, 89.488, 110.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 41701.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: TRP4, YDR354W, D9476.4 / Production host: Escherichia coli (E. coli)
References: UniProt: P07285, anthranilate phosphoribosyltransferase
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS PH 6.5, 16% W/V PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 29444 / % possible obs: 100 % / Redundancy: 13.1 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Net I/σ(I): 24.3
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 4 / Num. unique obs: 1440 / Rpim(I) all: 0.134 / Rrim(I) all: 0.484 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DSM

7dsm


Resolution: 2.44→46.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.965 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1401 4.8 %RANDOM
Rwork0.1803 ---
obs0.1832 27912 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.56 Å2 / Biso mean: 41.681 Å2 / Biso min: 23.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0 Å2
2--3.14 Å2-0 Å2
3----2.83 Å2
Refinement stepCycle: final / Resolution: 2.44→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 46 133 5678
Biso mean--67.38 41.25 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135668
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175288
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6377700
X-RAY DIFFRACTIONr_angle_other_deg1.3491.57412306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38423.767223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.00215947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0741512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021078
LS refinement shellResolution: 2.44→2.502 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.348 95 -
Rwork0.218 1893 -
obs--92.17 %

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