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

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Basic information

Entry
Database: PDB / ID: 4owm
TitleAnthranilate phosphoribosyl transferase from Mycobacterium tuberculosis in complex with 3-fluoroanthranilate, PRPP and Magnesium
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Anthranilic Acids / Magnesium / Tryptophan / Inhibitor
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / L-tryptophan biosynthetic process / magnesium ion binding / extracellular region / plasma membrane / 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
2-azanyl-3-fluoranyl-benzoic acid / IMIDAZOLE / Chem-PRP / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.99 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 2, 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_conn_angle / 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 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / refine_hist / 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 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 1.6Dec 27, 2023Group: 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)79,04712
Polymers77,6982
Non-polymers1,34910
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-86 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.274, 91.990, 120.892
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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
#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

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Non-polymers , 5 types, 461 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3F0 / 2-azanyl-3-fluoranyl-benzoic acid / 3-fluoroanthranilate


Mass: 155.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6FNO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 3.06 Å3/Da / Density % sol: 59.85 %
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: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.99→120.892 Å / Num. all: 52873 / Num. obs: 52873 / % possible obs: 86.9 % / Redundancy: 4.6 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.105 / Rsym value: 0.085 / Net I/av σ(I): 7.8 / Net I/σ(I): 12.2 / Num. measured all: 245631
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
1.99-2.14.50.4851.63588978890.2550.4852.890
2.1-2.234.60.3162.43411874200.1660.3164.289.3
2.23-2.384.60.2213.53212369550.1160.2216.188.5
2.38-2.574.70.1564.92994164140.0820.1568.387.8
2.57-2.824.70.1146.72746958610.060.11411.286.9
2.82-3.154.70.0799.32467352400.0410.07915.786
3.15-3.644.70.05612.22171646110.030.0562284.9
3.64-4.464.70.04414.71798138480.0240.04427.983.3
4.46-6.34.70.0415.61387129690.0220.0428.681.7
6.3-120.8924.70.03215.4785016660.0170.03232.179.2

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.99→73.21 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.072 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2677 5.1 %RANDOM
Rwork0.1704 50142 --
obs0.1725 52819 86.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.46 Å2 / Biso mean: 22.213 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å20 Å2
2--1.72 Å20 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.99→73.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4988 0 81 453 5522
Biso mean--35.26 33.36 -
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195196
X-RAY DIFFRACTIONr_bond_other_d0.0010.024980
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9637106
X-RAY DIFFRACTIONr_angle_other_deg0.773.00111342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92522.549204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87615722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4381551
X-RAY DIFFRACTIONr_chiral_restr0.0750.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021197
LS refinement shellResolution: 1.993→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 197 -
Rwork0.242 3797 -
all-3994 -
obs--89.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°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)
10.9015-0.20390.55780.2534-0.29120.5921-0.0358-0.13120.01830.00060.03190.00890.0166-0.07250.00390.01240.0105-0.00270.0242-0.00630.0052-20.7223-21.1159.2075
21.0573-0.22950.43960.1219-0.01940.5091-0.00950.07140.071-0.0161-0.0299-0.0379-0.04870.00340.03940.00730.00420.00160.00820.00780.01637.4067-24.289351.3319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 405
2X-RAY DIFFRACTION2B24 - 405

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