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- PDB-5cuu: Crystal structure of Trypanosoma cruzi Vacuolar Soluble Pyrophosp... -

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Basic information

Entry
Database: PDB / ID: 5cuu
TitleCrystal structure of Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in complex with bisphosphonate inhibitor BPH-1260
ComponentsAcidocalcisomal pyrophosphatase
KeywordsMETAL BINDING PROTEIN / substrate binding / acidocalcisomal pyrophosphatase / inhibitor
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / EF-hand domain pair
Similarity search - Domain/homology
Chem-4GA / D-MALATE / inorganic diphosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsLiu, W.D. / Yang, Y.Y. / Ko, T.P. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Crystal structure of Trypanosoma cruzi protein in complex with ligand
Authors: Yang, Y.Y. / Ko, T.P. / Zheng, Y.Y. / Liu, W.D. / Chen, C.C. / Guo, R.T.
History
DepositionJul 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Data collection
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9399
Polymers95,8302
Non-polymers1,1097
Water2,180121
1
A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules

A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,87818
Polymers191,6604
Non-polymers2,21914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area26010 Å2
ΔGint-150 kcal/mol
Surface area65170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.775, 102.630, 158.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acidocalcisomal pyrophosphatase


Mass: 47914.891 Da / Num. of mol.: 2 / Fragment: UNP residues 32-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4JH30
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-4GA / 1-butyl-3-(2-hydroxy-2,2-diphosphonoethyl)-1H-imidazol-3-ium


Mass: 329.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19N2O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.33 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: magnesium sulfate heptahydrate, tri-sodium citrate dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→25 Å / Num. obs: 17519 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Rrim(I) all: 0.07 / Χ2: 1.062 / Net I/av σ(I): 23.355 / Net I/σ(I): 12.8 / Num. measured all: 78125
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.96-3.074.50.517180.8740.2580.5651.014100
3.07-3.194.50.40117290.9050.2080.4531.059100
3.19-3.334.60.23717190.9680.1220.2671.081100
3.33-3.514.50.15617310.9840.0810.1771.04100
3.51-3.734.50.10817460.9940.0560.1221.088100
3.73-4.014.50.08217510.9960.0430.0931.10699.9
4.01-4.424.50.05917340.9970.0310.0671.07599.9
4.42-5.054.40.04117680.9980.0210.0460.983100
5.05-6.354.40.03317760.9990.0180.0381.079100
6.35-254.10.02318470.9990.0130.0271.09798.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNS1.21refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CUV

5cuv


Resolution: 2.96→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 815 4.7 %RANDOM
Rwork0.1939 15736 --
obs-16551 94.6 %-
Solvent computationBsol: 29.3696 Å2
Displacement parametersBiso max: 183.96 Å2 / Biso mean: 78.7563 Å2 / Biso min: 29.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.694 Å20 Å20 Å2
2---21.075 Å20 Å2
3---20.38 Å2
Refinement stepCycle: final / Resolution: 2.96→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6187 0 69 121 6377
Biso mean--117.14 59.75 -
Num. residues----757
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4561.5
X-RAY DIFFRACTIONc_scbond_it1.7382
X-RAY DIFFRACTIONc_mcangle_it2.5972
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 2.96→3.07 Å /
RfactorNum. reflection
Rfree0.363 -
Rwork0.308 1718
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2bph1260.par
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5mlt.par

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