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- PDB-5bo3: Bianthranilate-like inhibitor with 5 atom "line" and phosphonate ... -

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Basic information

Entry
Database: PDB / ID: 5bo3
TitleBianthranilate-like inhibitor with 5 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / complex / Lobenzarit-like analogue / TB Structural Genomics Consortium / TBSGC / magnesium binding / 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-7P2 / IMIDAZOLE / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsEvans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC)HRC12/1111 New Zealand
FRST (Foundation for Research, Science and Technology)UOAX1005 New Zealand
CitationJournal: To be Published
Title: Binding and mimicking of the phosphate-rich substrate, PRPP.
Authors: Evans, G.L. / Baker, E.N. / Lott, J.S.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,8536
Polymers77,8962
Non-polymers9574
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-15 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.038, 78.136, 102.643
Angle α, β, γ (deg.)90.00, 111.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-401-

IMD

21A-558-

HOH

31A-688-

HOH

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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 (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: trpD, MRA_2208 / Plasmid: pET23A / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) pLysS
References: UniProt: A5U4M0, anthranilate phosphoribosyltransferase
#2: Chemical ChemComp-7P2 / 2-[(2-carboxyphenyl)amino]-5-(4-phosphonobutoxy)benzoic acid


Mass: 409.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20NO8P
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.29 Å3/Da / Density % sol: 46.34 % / Description: Flat-diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M imidazole-malate, 11% PEG-4000

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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: Mar 26, 2015
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: 1.75→48 Å / Num. obs: 68993 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.762 / Mean I/σ(I) obs: 1.2 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
XDSNovember 3, 2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QR9 chain A

3qr9


Resolution: 1.75→47.231 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 3405 4.94 %Random selection
Rwork0.2057 ---
obs0.2074 68962 97.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 66 402 5145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054910
X-RAY DIFFRACTIONf_angle_d0.8996710
X-RAY DIFFRACTIONf_dihedral_angle_d12.191695
X-RAY DIFFRACTIONf_chiral_restr0.033781
X-RAY DIFFRACTIONf_plane_restr0.004885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.78020.33621690.31873152X-RAY DIFFRACTION95
1.7802-1.81260.32772040.2913200X-RAY DIFFRACTION97
1.8126-1.84750.35461520.28783237X-RAY DIFFRACTION96
1.8475-1.88520.35631760.30973202X-RAY DIFFRACTION97
1.8852-1.92620.41011540.37953287X-RAY DIFFRACTION97
1.9262-1.9710.30951590.24933226X-RAY DIFFRACTION97
1.971-2.02030.28131510.23383220X-RAY DIFFRACTION97
2.0203-2.07490.27121790.2283279X-RAY DIFFRACTION97
2.0749-2.1360.2351880.20263242X-RAY DIFFRACTION98
2.136-2.20490.24341520.20783302X-RAY DIFFRACTION97
2.2049-2.28370.32641560.25993292X-RAY DIFFRACTION98
2.2837-2.37510.23481750.19893264X-RAY DIFFRACTION98
2.3751-2.48320.22031760.19733273X-RAY DIFFRACTION98
2.4832-2.61410.23981530.19043292X-RAY DIFFRACTION98
2.6141-2.77790.25221640.19893331X-RAY DIFFRACTION98
2.7779-2.99230.22921790.20433295X-RAY DIFFRACTION99
2.9923-3.29340.2781730.20763328X-RAY DIFFRACTION99
3.2934-3.76980.19131980.18333324X-RAY DIFFRACTION99
3.7698-4.74890.18271620.15563395X-RAY DIFFRACTION99
4.7489-47.24810.18661850.16533416X-RAY DIFFRACTION99

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