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

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Basic information

Entry
Database: PDB / ID: 5kdf
TitleInorganic pyrophosphatase from Mycobacterium tuberculosis in complex with inhibitor 6 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-6RU / PYROPHOSPHATE 2- / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0596
Polymers19,4551
Non-polymers6055
Water48627
1
A: Inorganic pyrophosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)120,35736
Polymers116,7296
Non-polymers3,62730
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area18580 Å2
ΔGint-228 kcal/mol
Surface area36620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.972, 98.972, 97.571
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 sequence contains 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-6RU / ~{N}2,~{N}2,~{N}4,~{N}4-tetramethyl-6-(1-phenylpyrrol-2-yl)-1,3,5-triazine-2,4-diamine


Mass: 308.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


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


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.75 1.4 M K H2PO4 2 mM CaCl2

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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: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 10662 / % possible obs: 97.7 % / Redundancy: 11.8 % / Net I/σ(I): 29
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 12.2 % / % possible all: 99.8

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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: 2.45→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.052 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.199 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21763 520 4.9 %RANDOM
Rwork0.18644 ---
obs0.18798 10141 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 35 27 1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191352
X-RAY DIFFRACTIONr_bond_other_d0.0020.021242
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9871838
X-RAY DIFFRACTIONr_angle_other_deg0.90832857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.4723.91369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49515206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0471510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211534
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_it2.5684.342646
X-RAY DIFFRACTIONr_mcbond_other2.3224.342645
X-RAY DIFFRACTIONr_mcangle_it3.7556.473802
X-RAY DIFFRACTIONr_mcangle_other3.7536.483803
X-RAY DIFFRACTIONr_scbond_it2.8944.829704
X-RAY DIFFRACTIONr_scbond_other2.8144.774697
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7937.0121024
X-RAY DIFFRACTIONr_long_range_B_refined7.37935.6751444
X-RAY DIFFRACTIONr_long_range_B_other7.29535.5721438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.449→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 38 -
Rwork0.222 729 -
obs--98.97 %

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