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- PDB-3r88: Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 3r88
TitleAnthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex with inhibitor ACS145)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTransferase/Transferase Inhibitor / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Magnesium / Tryptophan / Inhibitor / Transferase / Magnesium binding Phosphoribosyl pyrophosphate / Transferase-Transferase Inhibitor complex
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
2-amino-4,5-dimethoxybenzoic acid / Chem-PRP / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsCastell, A. / Short, F.L. / Lott, J.S.
CitationJournal: Biochemistry / Year: 2013
Title: The Substrate Capture Mechanism of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Provides a Mode for Inhibition.
Authors: Castell, A. / Short, F.L. / Evans, G.L. / Cookson, T.V. / Bulloch, E.M. / Joseph, D.D. / Lee, C.E. / Parker, E.J. / Baker, E.N. / Lott, J.S.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Nov 27, 2013Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,60210
Polymers77,4352
Non-polymers1,1678
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-88 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.312, 78.849, 100.494
Angle α, β, γ (deg.)90.00, 110.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38717.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2248, MTCY190.03c, Rv2192c, trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P66992, UniProt: P9WFX5*PLUS, 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
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 695 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-14F / 2-amino-4,5-dimethoxybenzoic acid


Mass: 197.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M cacodylate, 9% PEG-6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.73→58.864 Å / Num. all: 71917 / Num. obs: 71917 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.065 / Net I/σ(I): 23.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.73-1.8270.6571.20.657199.2
1.82-1.937.10.4211.90.421199.6
1.93-2.077.20.2443.20.244199.9
2.07-2.237.30.1515.20.1511100
2.23-2.457.30.17.80.11100
2.45-2.747.40.07110.071100
2.74-3.167.50.04716.20.0471100
3.16-3.877.50.02923.70.0291100
3.87-5.477.40.02329.50.0231100
5.47-94.2727.30.02130.30.021199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→58.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.203 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1034 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21423 3564 5 %RANDOM
Rwork0.17548 ---
obs0.17742 68342 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.62 Å2
2---0.56 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.73→58.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 68 689 5733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225133
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9627010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60422.574202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34815718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4231550
X-RAY DIFFRACTIONr_chiral_restr0.090.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.53398
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38925374
X-RAY DIFFRACTIONr_scbond_it2.36131735
X-RAY DIFFRACTIONr_scangle_it3.8624.51636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 266 -
Rwork0.249 5006 -
obs--98.78 %

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