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- PDB-4x5b: Anthranilate phosphoribosyltransferase variant R193L from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4x5b
TitleAnthranilate phosphoribosyltransferase variant R193L from Mycobacterium tuberculosis in complex with PRPP and Mg
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Anthranilate Phosphoribosyltransferase / Anthranilic Acids / Mycobacterium tuberculosis / Magnesium / Tryptophan / mutation / Magnesium binding / Phosphoribosyl pyrophosphate
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-PRP / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsCookson, T.V.M. / Parker, E.J. / Lott, J.S.
CitationJournal: Biochemistry / Year: 2015
Title: Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site.
Authors: Cookson, T.V. / Evans, G.L. / Castell, A. / Baker, E.N. / Lott, J.S. / Parker, E.J.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,4386
Polymers77,6102
Non-polymers8294
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-64 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.420, 78.130, 100.430
Angle α, β, γ (deg.)90.000, 110.530, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38804.848 Da / Num. of mol.: 2 / Mutation: R193L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trpD / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U4M0, UniProt: P9WFX5*PLUS, anthranilate phosphoribosyltransferase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: imidazole malate, PEG 4000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.47→39.99 Å / Num. obs: 24299 / % possible obs: 98.8 % / Redundancy: 5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.093 / Net I/σ(I): 7.5 / Num. measured all: 121456 / Scaling rejects: 66
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.1 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.47-2.591.0811.91635732220.5690.54298.9
8.19-39.990.04220.535576990.9980.02197.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QR9

3qr9


Resolution: 2.47→39.99 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.468 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.695 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 1236 5.1 %RANDOM
Rwork0.2104 23059 --
obs0.2129 23059 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.99 Å2 / Biso mean: 34.384 Å2 / Biso min: 14.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-2.79 Å2
2---2.18 Å2-0 Å2
3---2.38 Å2
Refinement stepCycle: final / Resolution: 2.47→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 46 46 5028
Biso mean--54.27 33.71 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195076
X-RAY DIFFRACTIONr_bond_other_d0.0050.024836
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9576946
X-RAY DIFFRACTIONr_angle_other_deg0.736311017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8422.813192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83615688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3321544
X-RAY DIFFRACTIONr_chiral_restr0.0570.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 73 -
Rwork0.321 1716 -
all-1789 -
obs--98.68 %
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)
10.195-0.2340.2461.0617-0.31910.3449-0.017-0.0766-0.0173-0.12390.034-0.0217-0.0111-0.0496-0.01690.04530.02230.02650.1180.01260.02147.4766-47.714539.4315
20.1268-0.21060.10451.8049-0.44410.3562-0.02270.0201-0.01180.08320.0962-0.1091-0.0458-0.0633-0.07340.03050.00950.02390.09080.00730.060227.4557-12.18819.0113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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