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- PDB-4owv: Anthranilate phosphoribosyl transferase from Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 4owv
TitleAnthranilate phosphoribosyl transferase from Mycobacterium tuberculosis in complex with anthranilate
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Anthranilic Acids / Magnesium / Tryptophan / Inhibitor
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-AMINOBENZOIC ACID / PHOSPHATE ION / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsCastell, A. / Cookson, T.V.M. / Short, F.L. / Lott, J.S.
CitationJournal: Biochem.J. / Year: 2014
Title: Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis.
Authors: Cookson, T.V. / Castell, A. / Bulloch, E.M. / Evans, G.L. / Short, F.L. / Baker, E.N. / Lott, J.S. / Parker, E.J.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)78,1596
Polymers77,6982
Non-polymers4614
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-15 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.585, 91.735, 120.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38848.883 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: Chemical ChemComp-BE2 / 2-AMINOBENZOIC ACID


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: imidazole/malate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.03316 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.9→72.957 Å / Num. all: 69457 / Num. obs: 69457 / % possible obs: 99.3 % / Redundancy: 5 % / Rpim(I) all: 0.074 / Rrim(I) all: 0.171 / Rsym value: 0.153 / Net I/av σ(I): 3.413 / Net I/σ(I): 8.2 / Num. measured all: 344568
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-24.81.0470.448377100630.531.0471.899.7
2-2.124.90.580.94685995070.2790.583.199.4
2.12-2.2750.3282.24422588960.1550.3284.798.7
2.27-2.455.10.2083.44268383620.0960.2086.599.7
2.45-2.6950.1564.63903377500.0730.1568.499.8
2.69-35.10.1165.93550470050.0540.11610.799.3
3-3.4750.0916.73089762050.0440.09113.999.4
3.47-4.254.90.087.52548352340.0390.0816.898.7
4.25-6.014.90.0767.42015541040.0380.07617.198.7
6.01-120.354.90.0677.61135223310.0320.06717.397.4

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.9→42.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.105 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 3444 5 %RANDOM
Rwork0.1932 65904 --
obs0.1946 69348 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 20.199 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0 Å20 Å2
2--1.09 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.9→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4955 0 31 485 5471
Biso mean--41.28 31.35 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195086
X-RAY DIFFRACTIONr_bond_other_d0.0010.024913
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9536942
X-RAY DIFFRACTIONr_angle_other_deg0.798311173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83422.525198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51215709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5861549
X-RAY DIFFRACTIONr_chiral_restr0.0790.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021176
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 253 -
Rwork0.406 4786 -
all-5039 -
obs--98.78 %
Refinement TLS params.

L12: -0.1945 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.777-0.32740.05170.05840.5239-0.02660.0687-0.05840.0033-0.01990.01950.0845-0.00550.04650.01580.00090.01030.0091-0.00950.0291-6.817824.3232-8.8914
20.5559-0.28080.22660.13060.5106-0.0103-0.07650.00690.00280.0192-0.0041-0.02830.06-0.00890.00340.00020.00070.0224-0.00390.008920.463121.248-51.2442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 420
2X-RAY DIFFRACTION2B1 - 420

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