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- PDB-7dsp: Anthranilate phosphoribosyltransferase variant Ser121Ala from Sac... -

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Basic information

Entry
Database: PDB / ID: 7dsp
TitleAnthranilate phosphoribosyltransferase variant Ser121Ala from Saccharomyces cerevisiae with Mg bound
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Tryptophan biosynthesis / anthranilate phosphoribosyltransferase activity
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
Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
B: Anthranilate phosphoribosyltransferase
A: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6964
Polymers83,6482
Non-polymers492
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-34 kcal/mol
Surface area27130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.164, 87.002, 108.433
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: 41823.773 Da / Num. of mol.: 2 / Mutation: S121A
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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 18 % MPEG 5000, 0.1 M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 55409 / % possible obs: 100 % / Redundancy: 13 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 32.2
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2737 / Rpim(I) all: 0.143 / Rrim(I) all: 0.517 / % 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: 1.95→46.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.275 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 2726 4.9 %RANDOM
Rwork0.1635 ---
obs0.1657 52587 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.4 Å2 / Biso mean: 29.652 Å2 / Biso min: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--1.19 Å2-0 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 1.95→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 2 442 5917
Biso mean--31.14 36.81 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135597
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175251
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.6257593
X-RAY DIFFRACTIONr_angle_other_deg1.461.57112212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41823.833227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90215947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3591512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021071
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.23 190 -
Rwork0.192 3840 -
obs--99.78 %

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