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- PDB-4x5e: Anthranilate phosphoribosyltransferase variant R194A from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 4x5e
TitleAnthranilate phosphoribosyltransferase variant R194A from Mycobacterium tuberculosis with pyrophosphate, Mg2+ and anthranilate bound
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
2-AMINOBENZOIC ACID / PYROPHOSPHATE 2- / Anthranilate phosphoribosyltransferase / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsCookson, T.V.M. / Evans, G.L. / 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 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_1

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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)78,98417
Polymers77,5262
Non-polymers1,45815
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-19 kcal/mol
Surface area26390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.938, 78.564, 101.318
Angle α, β, γ (deg.)90.000, 110.180, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Anthranilate phosphoribosyltransferase /


Mass: 38762.766 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 535 molecules

#2: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-BE2 / 2-AMINOBENZOIC ACID / Anthranilic acid


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7NO2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 278 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: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→95.097 Å / Num. all: 68018 / Num. obs: 68018 / % possible obs: 99.9 % / Redundancy: 12.2 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.141 / Rsym value: 0.136 / Net I/av σ(I): 4.487 / Net I/σ(I): 12 / Num. measured all: 832265
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.77-1.879.12.2840.39021398690.7492.2841.299.4
1.87-1.9810.11.2750.69381593290.4031.2752.199.7
1.98-2.1211.10.711.19793188130.2170.713.999.9
2.12-2.2912.10.4231.89943982040.1250.4236.5100
2.29-2.513.20.2732.89934575520.0780.2739.5100
2.5-2.8140.1814.19670668860.050.18114100
2.8-3.2314.60.1175.98791860250.0320.11720.7100
3.23-3.9614.60.0787.97461951120.0210.07831.9100
3.96-5.614.80.0629.55910440040.0170.06237.4100
5.6-95.09714.90.0539.33317522240.0140.05339.9100

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Processing

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

3qr9


Resolution: 1.77→95.097 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.865 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 3402 5 %RANDOM
Rwork0.1855 64604 --
obs0.1873 64604 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.53 Å2 / Biso mean: 28.475 Å2 / Biso min: 12.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-1.06 Å2
2---1.54 Å20 Å2
3---1.62 Å2
Refinement stepCycle: final / Resolution: 1.77→95.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4969 0 92 520 5581
Biso mean--42.11 37.68 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195210
X-RAY DIFFRACTIONr_bond_other_d0.0010.025048
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9637111
X-RAY DIFFRACTIONr_angle_other_deg0.79311485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52422.271207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26415736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2851555
X-RAY DIFFRACTIONr_chiral_restr0.0760.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021226
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 256 -
Rwork0.394 4736 -
all-4992 -
obs--99.03 %
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)
10.01540.02470.02050.14840.04580.0511-0.0041-0.0008-0.0016-0.01310.01090.0061-0.00410.0093-0.00680.0094-0.00160.00720.0208-0.00130.00962.41738.206638.5686
20.0720.05090.04750.14560.07590.0490.00070.0147-0.00420.02080.0031-0.00120.00590.0107-0.00380.0111-0.00340.0050.0228-0.00040.0036-17.7675-27.27167.5223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 371
2X-RAY DIFFRACTION2B24 - 370

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