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- PDB-7ddv: Crystal structure of M.tuberculosis imidazole glycerol phosphate ... -

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Basic information

Entry
Database: PDB / ID: 7ddv
TitleCrystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE/LYASE INHIBITOR / Inhibitor / LYASE / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
(1S)-1-(2-methyl-1,2,4-triazol-3-yl)ethanamine / : / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTiwari, S. / Pal, R.K. / Biswal, B.K.
CitationJournal: To Be Published
Title: Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor
Authors: Tiwari, S. / Pal, R.K. / Biswal, B.K.
History
DepositionOct 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0337
Polymers23,6341
Non-polymers3996
Water2,252125
1
A: Imidazoleglycerol-phosphate dehydratase
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)576,781168
Polymers567,20424
Non-polymers9,577144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area102100 Å2
ΔGint-653 kcal/mol
Surface area124510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.829, 111.829, 111.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-305-

CL

21A-501-

HOH

31A-521-

HOH

41A-525-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Imidazoleglycerol-phosphate dehydratase / / IGPD


Mass: 23633.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: hisB, Rv1601, MTCY336.03c / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: P9WML9, imidazoleglycerol-phosphate dehydratase

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Non-polymers , 5 types, 131 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-H3L / (1S)-1-(2-methyl-1,2,4-triazol-3-yl)ethanamine


Mass: 126.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 9
Details: 20% PEG1500, 0.2M sodium citrate tribasic dehydrate, 0.1M Tris HCL, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 12742 / % possible obs: 100 % / Redundancy: 21.5 % / CC1/2: 0.92 / Net I/σ(I): 13.56
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 1230 / CC1/2: 0.718

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GQU

4gqu


Resolution: 2.2→33.74 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.034 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2048 628 4.929 %
Rwork0.1557 12114 -
all0.158 --
obs-12742 99.922 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.539 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 19 125 1601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131515
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171395
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.6542066
X-RAY DIFFRACTIONr_angle_other_deg1.3581.5833209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4915195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1720.34986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45415227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.531515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
X-RAY DIFFRACTIONr_nbd_refined0.1970.2308
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21324
X-RAY DIFFRACTIONr_nbtor_refined0.1540.2714
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.227
X-RAY DIFFRACTIONr_nbd_other0.2140.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.215
X-RAY DIFFRACTIONr_mcbond_it1.7162.441765
X-RAY DIFFRACTIONr_mcbond_other1.7082.435764
X-RAY DIFFRACTIONr_mcangle_it2.6423.645956
X-RAY DIFFRACTIONr_mcangle_other2.6413.652957
X-RAY DIFFRACTIONr_scbond_it2.4162.749750
X-RAY DIFFRACTIONr_scbond_other2.4152.753751
X-RAY DIFFRACTIONr_scangle_it3.8313.9981107
X-RAY DIFFRACTIONr_scangle_other3.8294.0021108
X-RAY DIFFRACTIONr_lrange_it5.18129.2771638
X-RAY DIFFRACTIONr_lrange_other5.15328.9631613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2560.349390.274877X-RAY DIFFRACTION100
2.256-2.3180.284550.25844X-RAY DIFFRACTION100
2.318-2.3850.281500.216810X-RAY DIFFRACTION100
2.385-2.4580.209400.202803X-RAY DIFFRACTION100
2.458-2.5390.202340.18788X-RAY DIFFRACTION100
2.539-2.6280.193410.171745X-RAY DIFFRACTION100
2.628-2.7270.221370.164758X-RAY DIFFRACTION100
2.727-2.8380.216250.155704X-RAY DIFFRACTION100
2.838-2.9640.171310.126680X-RAY DIFFRACTION100
2.964-3.1090.128360.128653X-RAY DIFFRACTION100
3.109-3.2770.252330.154627X-RAY DIFFRACTION100
3.277-3.4750.203270.15591X-RAY DIFFRACTION100
3.475-3.7150.222350.13555X-RAY DIFFRACTION100
3.715-4.0120.151270.125531X-RAY DIFFRACTION100
4.012-4.3950.164300.111489X-RAY DIFFRACTION100
4.395-4.9130.164250.109441X-RAY DIFFRACTION100
4.913-5.6710.237180.131411X-RAY DIFFRACTION100
5.671-6.9410.171200.15346X-RAY DIFFRACTION100
6.941-9.7970.203130.147285X-RAY DIFFRACTION100
9.797-33.70.26120.204178X-RAY DIFFRACTION95

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