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- PDB-5kde: Inorganic pyrophosphatase from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 5kde
TitleInorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 1 and inorganic pyrophosphate
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / pyrophosphatase / drug target / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / host cell surface / magnesium ion binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-6RT / PYROPHOSPHATE 2- / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsPang, A.H. / Garzan, A. / Garneau-Tsodikova, S. / Tsodikov, O.V.
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase from Mycobacterium tuberculosis.
Authors: Pang, A.H. / Garzan, A. / Larsen, M.J. / McQuade, T.J. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9353
Polymers19,4551
Non-polymers4802
Water28816
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)119,61118
Polymers116,7296
Non-polymers2,88212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_535-y,x-y-2,z1
crystal symmetry operation3_755-x+y+2,-x,z1
crystal symmetry operation10_557-y,-x,-z+5/21
crystal symmetry operation11_757-x+y+2,y,-z+5/21
crystal symmetry operation12_537x,x-y-2,-z+5/21
Buried area15130 Å2
ΔGint-57 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.965, 99.965, 97.559
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 19454.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The expressed sequence includes a hexahistidine tag.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ppa, Rv3628, MTCY15C10.24 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WI55, inorganic diphosphatase
#2: Chemical ChemComp-6RT / 2,4-bis(aziridin-1-yl)-6-(1-phenylpyrrol-2-yl)-1,3,5-triazine


Mass: 304.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N6
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.62 Å3/Da / Density % sol: 65.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 1.6 M NaH2PO4, and 0.2 M KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 8828 / % possible obs: 99.6 % / Redundancy: 6.8 % / Net I/σ(I): 29
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z72

4z72


Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.639 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24015 424 4.8 %RANDOM
Rwork0.20399 ---
obs0.20578 8404 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.261 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å2-0 Å2
3----3.28 Å2
Refinement stepCycle: 1 / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 32 16 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191348
X-RAY DIFFRACTIONr_bond_other_d0.0010.021235
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9891837
X-RAY DIFFRACTIONr_angle_other_deg1.07532844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04723.82468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98815204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9371510
X-RAY DIFFRACTIONr_chiral_restr0.0650.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2255.697643
X-RAY DIFFRACTIONr_mcbond_other1.2255.692642
X-RAY DIFFRACTIONr_mcangle_it2.2378.543803
X-RAY DIFFRACTIONr_mcangle_other2.2378.543803
X-RAY DIFFRACTIONr_scbond_it0.9875.889704
X-RAY DIFFRACTIONr_scbond_other0.9825.856697
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.848.6881016
X-RAY DIFFRACTIONr_long_range_B_refined3.72145.0111383
X-RAY DIFFRACTIONr_long_range_B_other3.72244.9381381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.647→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 31 -
Rwork0.28 601 -
obs--99.68 %

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