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- PDB-5byt: PRPP complexed with a single Mg in the active site of Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 5byt
TitlePRPP complexed with a single Mg in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PRPP / phosphoriboysl pyrophosphate / TB Structural Genomics Consortium / TBSGC / magnesium binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
Chem-PRP / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEvans, G.L. / Baker, E.N. / Lott, J.S. / TB Structural Genomics Consortium (TBSGC)
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Health Research Council (HRC)HRC12/1111 New Zealand
FRST (Foundation for Research, Science and Technology)UOAX1005 New Zealand
CitationJournal: To be Published
Title: Binding and mimicking of the phosphate-rich substrate, PRPP.
Authors: Evans, G.L. / Baker, E.N. / Lott, J.S.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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_alt_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_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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 1.4Sep 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)78,7256
Polymers77,8962
Non-polymers8294
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-66 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.011, 81.192, 78.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 38948.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: trpD, Rv2192c, MTCY190.03c / Plasmid: pET23A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41(DE3)pLysS
References: UniProt: P9WFX5, anthranilate phosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: Flat-diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M imidazole-malate, 15% PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 27, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 49191 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.175 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.176 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
XDSNovember 3, 2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QR9 CHAIN A

3qr9


Resolution: 2→39.29 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2470 5.03 %Random selection
Rwork0.223 ---
obs0.225 49059 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 46 347 5324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035231
X-RAY DIFFRACTIONf_angle_d0.7147177
X-RAY DIFFRACTIONf_dihedral_angle_d11.2071816
X-RAY DIFFRACTIONf_chiral_restr0.028828
X-RAY DIFFRACTIONf_plane_restr0.003952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.3041330.28383091X-RAY DIFFRACTION100
2.0465-2.09770.30551360.26173108X-RAY DIFFRACTION100
2.0977-2.15440.31871620.25783057X-RAY DIFFRACTION100
2.1544-2.21780.35291670.28733056X-RAY DIFFRACTION100
2.2178-2.28940.40491660.34363066X-RAY DIFFRACTION100
2.2894-2.37120.3061950.24693029X-RAY DIFFRACTION100
2.3712-2.46610.29541700.23433092X-RAY DIFFRACTION100
2.4661-2.57830.27991700.22423068X-RAY DIFFRACTION100
2.5783-2.71430.26341690.22983087X-RAY DIFFRACTION100
2.7143-2.88430.30651550.22423110X-RAY DIFFRACTION100
2.8843-3.10690.31171860.2223089X-RAY DIFFRACTION100
3.1069-3.41940.28481720.21953113X-RAY DIFFRACTION100
3.4194-3.91380.26961380.19713159X-RAY DIFFRACTION100
3.9138-4.92940.19961660.1713186X-RAY DIFFRACTION100
4.9294-39.29660.16711850.17673278X-RAY DIFFRACTION99

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