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- PDB-3t44: Crystal structure of Mycobacterium tuberculosis Indole Glycerol P... -

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Basic information

Entry
Database: PDB / ID: 3t44
TitleCrystal structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in complex with indole glycerol phosphate (IGP) amd anthranilate
ComponentsIndole-3-glycerol phosphate synthase
KeywordsTRANSFERASE / Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) / Tryptophan biosynthesis / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


5-phosphoribose 1-diphosphate metabolic process / indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / L-tryptophan biosynthetic process / peptidoglycan-based cell wall / magnesium ion binding / plasma membrane
Similarity search - Function
Indole-3-glycerol phosphate synthase, conserved site / Indole-3-glycerol phosphate synthase signature. / Indole-3-glycerol phosphate synthase domain / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-AMINOBENZOIC ACID / INDOLE-3-GLYCEROL PHOSPHATE / Indole-3-glycerol phosphate synthase / Indole-3-glycerol phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsReddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Structural Insights and Inhibition of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS): an Essential Enzyme for Tryptophan Biosynthesis
Authors: Reddy, M.C.M. / Bruning, J.B. / Thurman, C. / Sacchettini, J.C.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Indole-3-glycerol phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4773
Polymers28,0531
Non-polymers4242
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.553, 53.222, 86.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Indole-3-glycerol phosphate synthase / IGPS


Mass: 28053.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1646, MTCY01B2.03, Rv1611, trpC / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A632, UniProt: P9WFX7*PLUS, indole-3-glycerol-phosphate synthase
#2: Chemical ChemComp-IGP / INDOLE-3-GLYCEROL PHOSPHATE


Mass: 287.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14NO6P
#3: Chemical ChemComp-BE2 / 2-AMINOBENZOIC ACID


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 1.92 Å3/Da / Density % sol: 35.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium acetate trihydrate, 2.0 ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9771 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 2, 2009 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9771 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 28784 / Num. obs: 28784 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Χ2: 2.34 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.6-1.637.20.4545.4813900.4541.617100
1.63-1.667.20.4126.1914340.4541.659100
1.66-1.697.20.3946.7614040.3941.797100
1.69-1.727.20.3657.3614300.3941.82499.9
1.72-1.767.20.3258.4414260.3251.84199.9
1.76-1.87.20.28510.2614120.2852.069100
1.8-1.857.20.27211.0714240.2722.2100
1.85-1.97.10.24413.0514290.2442.456100
1.9-1.957.10.21715.2514210.2172.688100
1.95-2.027.10.19616.8714200.1962.612100
2.02-2.097.10.1818.5914290.182.88799.9
2.09-2.1770.16320.7114270.1632.945100
2.17-2.2770.15621.8114370.1562.918100
2.27-2.397.10.14223.1414360.1422.873100
2.39-2.5470.1324.3914620.132.877100
2.54-2.7470.11625.3914400.1162.695100
2.74-3.016.90.10426.6814560.1042.529100
3.01-3.457.10.09329.0314660.0932.63799.9
3.45-4.347.20.0829.5814970.082.18799.9
4.34-506.60.06225.6215440.0621.52796.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IGS

1igs


Resolution: 1.6→26.61 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1988 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8834 / SU B: 3.514 / SU ML: 0.056 / SU R Cruickshank DPI: 0.1319 / SU Rfree: 0.0909 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1464 5.1 %RANDOM
Rwork0.1482 ---
obs0.1505 28717 98.68 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.38 Å2 / Biso mean: 20.7094 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 29 292 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221944
X-RAY DIFFRACTIONr_bond_other_d0.0020.021267
X-RAY DIFFRACTIONr_angle_refined_deg1.2872.0042659
X-RAY DIFFRACTIONr_angle_other_deg0.8893.0013092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8595272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82223.08868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3315307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7611519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02366
X-RAY DIFFRACTIONr_nbd_refined0.2160.2457
X-RAY DIFFRACTIONr_nbd_other0.2070.21446
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2988
X-RAY DIFFRACTIONr_nbtor_other0.0950.21063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.241
X-RAY DIFFRACTIONr_mcbond_it1.0261.51352
X-RAY DIFFRACTIONr_mcbond_other0.4061.5535
X-RAY DIFFRACTIONr_mcangle_it1.51622092
X-RAY DIFFRACTIONr_scbond_it2.5193654
X-RAY DIFFRACTIONr_scangle_it3.6074.5562
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 100 -
Rwork0.157 1692 -
all-1792 -
obs--84.77 %

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