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- PDB-5bne: Bianthranilate-like inhibitor with 6 atom "line" and phosphonate ... -

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Basic information

Entry
Database: PDB / ID: 5bne
TitleBianthranilate-like inhibitor with 6 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 / TrpD / AnPRT / 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 / 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
Chem-7P3 / IMIDAZOLE / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: 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 ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name / _software.version
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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
C: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,33811
Polymers155,7924
Non-polymers1,5467
Water6,359353
1
A: Anthranilate phosphoribosyltransferase
B: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9507
Polymers77,8962
Non-polymers1,0545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-12 kcal/mol
Surface area24840 Å2
MethodPISA
2
C: Anthranilate phosphoribosyltransferase
D: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3884
Polymers77,8962
Non-polymers4922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-16 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.300, 78.400, 117.200
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Anthranilate phosphoribosyltransferase


Mass: 38948.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: trpD, Rv2192c, MTCY190.03c / Plasmid: pET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WFX5, anthranilate phosphoribosyltransferase
#2: Chemical ChemComp-7P3 / 2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid


Mass: 423.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H22NO8P
#3: Chemical
ChemComp-IMD / IMIDAZOLE


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


Mass: 18.015 Da / Num. of mol.: 353 / 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: 46.27 % / Description: Flat-diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M imidazole-malate, 15% PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 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: 2.15→47 Å / Num. obs: 75079 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNovember 3, 2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QR9 chain A

3qr9


Resolution: 2.15→46.972 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3613 4.81 %Random selection
Rwork0.2066 ---
obs0.208 75043 98.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→46.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9280 0 107 353 9740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039570
X-RAY DIFFRACTIONf_angle_d0.74513083
X-RAY DIFFRACTIONf_dihedral_angle_d12.1433171
X-RAY DIFFRACTIONf_chiral_restr0.0271540
X-RAY DIFFRACTIONf_plane_restr0.0031724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.19140.33191790.28353909X-RAY DIFFRACTION97
2.1914-2.23610.28322010.26324019X-RAY DIFFRACTION100
2.2361-2.28470.28662000.25763980X-RAY DIFFRACTION99
2.2847-2.33790.29621780.24174040X-RAY DIFFRACTION100
2.3379-2.39630.30821870.24063985X-RAY DIFFRACTION99
2.3963-2.46110.292120.24063962X-RAY DIFFRACTION99
2.4611-2.53350.27172520.23143961X-RAY DIFFRACTION99
2.5335-2.61530.29341850.22664000X-RAY DIFFRACTION99
2.6153-2.70880.25942010.22323975X-RAY DIFFRACTION99
2.7088-2.81720.24952040.22833974X-RAY DIFFRACTION99
2.8172-2.94540.24011940.22183961X-RAY DIFFRACTION99
2.9454-3.10060.23362400.21753958X-RAY DIFFRACTION98
3.1006-3.29490.24861880.21763967X-RAY DIFFRACTION98
3.2949-3.54920.24921750.20623996X-RAY DIFFRACTION98
3.5492-3.90620.18891490.1824004X-RAY DIFFRACTION97
3.9062-4.47110.21511730.16343938X-RAY DIFFRACTION97
4.4711-5.63160.18382540.17493889X-RAY DIFFRACTION96
5.6316-46.98290.19152410.17433912X-RAY DIFFRACTION95

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