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- PDB-4x5a: Anthranilate phosphoribosyltransferase variant R193A from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4x5a
TitleAnthranilate phosphoribosyltransferase variant R193A from Mycobacterium tuberculosis remains ligand-free when co-crystallised with PRPP and Mg
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Mycobacterium tuberculosis / Magnesium / Tryptophan / mutation / Magnesium binding / Phosphoribosyl pyrophosphate
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / 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 / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCookson, T.V.M. / Parker, E.J. / Lott, J.S.
CitationJournal: Biochemistry / Year: 2015
Title: Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site.
Authors: Cookson, T.V. / Evans, G.L. / Castell, A. / Baker, E.N. / Lott, J.S. / Parker, E.J.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)77,9867
Polymers77,5262
Non-polymers4605
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-19 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.448, 77.779, 101.932
Angle α, β, γ (deg.)90.000, 111.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-507-

HOH

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38762.766 Da / Num. of mol.: 2 / Mutation: R193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U4M0, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: imidazole malate, PEG 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.93→47.31 Å / Num. obs: 50966 / % possible obs: 99 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.067 / Net I/σ(I): 8.2 / Num. measured all: 239508
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.93-1.984.71.6630.91687735640.560.85298.3
8.84-47.3140.04326.622585620.9960.02598.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QR9

3qr9


Resolution: 1.93→47.35 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.771 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2839 2586 5.1 %RANDOM
Rwork0.2384 48357 --
obs0.2407 48357 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.03 Å2 / Biso mean: 31.293 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-2.11 Å2
2---1.81 Å20 Å2
3---1.53 Å2
Refinement stepCycle: final / Resolution: 1.93→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 30 148 5127
Biso mean--45.02 31.5 -
Num. residues----695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195085
X-RAY DIFFRACTIONr_bond_other_d0.0010.024898
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9526941
X-RAY DIFFRACTIONr_angle_other_deg0.81311161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3045697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00422.684190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14415701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831545
X-RAY DIFFRACTIONr_chiral_restr0.0760.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 171 -
Rwork0.384 3577 -
all-3748 -
obs--98.12 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04990.08610.07710.59250.09390.14590.0021-0.00670.0044-0.060.01780.0317-0.00510.021-0.01990.0307-0.00450.02910.0875-0.00490.05141.20487.183938.5059
20.14560.07140.14640.66020.14740.15860.00180.0225-0.01250.05730.01110.00240.00530.0116-0.01290.0168-0.0070.0180.087-0.01220.0268-17.9152-27.24657.4229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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