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

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Basic information

Entry
Database: PDB / ID: 4owq
TitleAnthranilate phosphoribosyl transferase from Mycobacterium tuberculosis in complex with 3-methylanthranilate, PRPP and Magnesium
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-azanyl-3-methyl-benzoic acid / IMIDAZOLE / Chem-PRP / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 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 3, 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)79,10612
Polymers77,6982
Non-polymers1,40910
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-74 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.351, 92.268, 121.681
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

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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, 518 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3M0 / 2-azanyl-3-methyl-benzoic acid / 3-methylanthranilate


Mass: 151.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H9NO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / 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.: 510 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
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: 1.89→121.681 Å / Num. all: 71647 / Num. obs: 71647 / % possible obs: 100 % / Redundancy: 7.3 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Rsym value: 0.072 / Net I/av σ(I): 8.5 / Net I/σ(I): 17.8 / Num. measured all: 519744
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
1.89-27.10.481.672989103270.2110.483.5100
2-2.127.40.2942.67196397640.1260.2945.9100
2.12-2.267.40.19246820192470.0820.1929100
2.26-2.457.40.1375.56320085750.0590.13712.4100
2.45-2.687.40.17.55825879260.0430.116.7100
2.68-37.30.0739.95294772130.0310.07322.3100
3-3.467.30.05112.84655164090.0220.05130.8100
3.46-4.247.20.041153890954290.0180.04139.7100
4.24-5.9970.03716.22977142710.0160.03741.7100
5.99-121.6816.80.03215.81695524860.0140.03244.399.9

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.89→73.52 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.6 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 3630 5.1 %RANDOM
Rwork0.1678 67939 --
obs0.169 71569 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.39 Å2 / Biso mean: 22.336 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0 Å20 Å2
2--1.59 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.89→73.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 86 510 5570
Biso mean--31.76 34.47 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195172
X-RAY DIFFRACTIONr_bond_other_d0.0020.024963
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9647072
X-RAY DIFFRACTIONr_angle_other_deg0.7963.00111299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5175695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34722.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73715713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.851549
X-RAY DIFFRACTIONr_chiral_restr0.080.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021183
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 267 -
Rwork0.245 4941 -
all-5208 -
obs--99.83 %
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)
10.8347-0.24510.5760.3011-0.26770.6316-0.0252-0.11960.00670.00870.02530.01460.02-0.0714-0.00010.00980.007-0.00160.0207-0.00430.0038-20.6387-21.08199.1686
20.9527-0.21170.38610.0948-0.00810.4697-0.01660.05050.072-0.0229-0.0232-0.0378-0.0682-0.00850.03990.03230.0051-0.00090.00650.00810.03037.3799-24.346151.6924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 420
2X-RAY DIFFRACTION2B1 - 420

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