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- PDB-4zok: Methylsulfonyl-containing inhibitor bound in the substrate captur... -

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Basic information

Entry
Database: PDB / ID: 4zok
TitleMethylsulfonyl-containing inhibitor bound in the substrate capture site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor / complex / Lobenzarit-like analogue / TB Structural Genomics Consortium / TBSGC / phosphoribosyltransferase / magnesium binding / phosphoribosylpyrophosphate / PRPP / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / L-tryptophan biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / 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 / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / 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
Chem-62L / Chem-PRP / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsEvans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Biopharma TRI fund76673 New Zealand
Health Research Council (HRC)12/110C New Zealand
CitationJournal: To be Published
Title: Inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD).
Authors: Evans, G.L. / Baker, E.N. / Lott, J.S.
History
DepositionMay 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / 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_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_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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)79,0939
Polymers77,8962
Non-polymers1,1977
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-89 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 77.700, 101.500
Angle α, β, γ (deg.)90.00, 110.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38948.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: trpD, MRA_2208 / Plasmid: pET23A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pGroESL
References: UniProt: A5U4M0, anthranilate phosphoribosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-62L / 4-methyl-2-{[2-methyl-6-(methylsulfonyl)phenyl]amino}benzoic acid


Mass: 319.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NO4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.25 % / Description: Flat diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M imidazole-malate, 11% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 30, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.34→36 Å / Num. obs: 29113 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.214 / Net I/σ(I): 4.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5refinement
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QR9 chain A

3qr9


Resolution: 2.34→35.497 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1444 4.96 %Random selection
Rwork0.202 ---
obs0.205 29113 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→35.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 70 110 4966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024964
X-RAY DIFFRACTIONf_angle_d0.5666808
X-RAY DIFFRACTIONf_dihedral_angle_d9.7551656
X-RAY DIFFRACTIONf_chiral_restr0.023805
X-RAY DIFFRACTIONf_plane_restr0.002892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.42360.32021320.2542758X-RAY DIFFRACTION100
2.4236-2.52060.3011370.26492754X-RAY DIFFRACTION100
2.5206-2.63530.3741390.25352761X-RAY DIFFRACTION100
2.6353-2.77420.3061490.25252781X-RAY DIFFRACTION100
2.7742-2.94790.28421330.2332741X-RAY DIFFRACTION100
2.9479-3.17540.30841560.23522730X-RAY DIFFRACTION100
3.1754-3.49470.2881410.21612769X-RAY DIFFRACTION100
3.4947-3.99980.22131630.18032762X-RAY DIFFRACTION100
3.9998-5.03710.23441380.15822789X-RAY DIFFRACTION100
5.0371-35.50060.20521560.15832824X-RAY DIFFRACTION100

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