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- PDB-5c1r: Stereoisomer of PRPP bound in the active site of Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 5c1r
TitleStereoisomer of PRPP bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyl (AnPRT; trpD)
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Stereoisomer of PRPP / phosphoriboysl pyrophosphate / TB Structural Genomics Consortium / TBSGC / magnesium binding / PSI-2 / Protein Structure Initiative
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-51N / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 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 15, 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 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _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 / _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 2.1Sep 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)78,8659
Polymers77,8962
Non-polymers9697
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-55 kcal/mol
Surface area25310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.301, 78.490, 100.485
Angle α, β, γ (deg.)90.00, 110.41, 90.00
Int Tables number5
Space group name H-MC121

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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): BL21(DE3)pGroESL
References: UniProt: P9WFX5, anthranilate phosphoribosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-51N / 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribofuranose / 1'-ALPHA-PHOSPHORIBOSYL-5'-PYROPHOSPHORIC ACID / 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribose / 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-D-ribose / 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.25 Å3/Da / Density % sol: 45.3 % / Description: square-diamond shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: Jun 15, 2012
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: 1.8→48 Å / Num. obs: 61658 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.3 / % possible all: 65.1

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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: 1.802→47.088 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 3117 5.06 %Random selection
Rwork0.1723 ---
obs0.1742 61653 97.23 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→47.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 54 500 5512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085194
X-RAY DIFFRACTIONf_angle_d1.1597107
X-RAY DIFFRACTIONf_dihedral_angle_d11.6151809
X-RAY DIFFRACTIONf_chiral_restr0.043822
X-RAY DIFFRACTIONf_plane_restr0.006944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8024-1.84430.27941770.23622664X-RAY DIFFRACTION67
1.8443-1.89040.25431640.20693710X-RAY DIFFRACTION93
1.8904-1.94150.24681950.18253938X-RAY DIFFRACTION98
1.9415-1.99870.2161800.17334015X-RAY DIFFRACTION100
1.9987-2.06320.22612240.17853993X-RAY DIFFRACTION100
2.0632-2.13690.23052070.17084014X-RAY DIFFRACTION100
2.1369-2.22250.21652180.17083998X-RAY DIFFRACTION100
2.2225-2.32360.22192170.16813995X-RAY DIFFRACTION100
2.3236-2.44610.24021880.17494056X-RAY DIFFRACTION100
2.4461-2.59940.22911910.17414006X-RAY DIFFRACTION100
2.5994-2.80010.2062530.1833988X-RAY DIFFRACTION100
2.8001-3.08180.21062150.18164013X-RAY DIFFRACTION100
3.0818-3.52760.20842070.18224031X-RAY DIFFRACTION100
3.5276-4.44390.18782350.15264030X-RAY DIFFRACTION100
4.4439-47.10440.16712460.15764085X-RAY DIFFRACTION100

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