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- PDB-5cux: Crystal structure of N-terminal domain truncated Trypanosoma cruz... -

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Basic information

Entry
Database: PDB / ID: 5cux
TitleCrystal structure of N-terminal domain truncated Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in complex with PPi
ComponentsAcidocalcisomal pyrophosphatase
KeywordsMETAL BINDING PROTEIN / substrate binding / acidocalcisomal pyrophosphatase
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 / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / EF-hand domain pair / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / PYROPHOSPHATE 2- / inorganic diphosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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)62,36112
Polymers61,1682
Non-polymers1,19310
Water2,126118
1
A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules

A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,72224
Polymers122,3374
Non-polymers2,38520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area18950 Å2
ΔGint-189 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.893, 122.893, 127.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Acidocalcisomal pyrophosphatase


Mass: 30584.229 Da / Num. of mol.: 2 / Fragment: UNP residues 147-408
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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 4.55 Å3/Da / Density % sol: 72.97 %
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 27934 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Χ2: 1.49 / Net I/av σ(I): 42.501 / Net I/σ(I): 18.2 / Num. measured all: 204818
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.97.50.49527410.9120.1930.5321.242100
2.9-3.027.50.35127660.9520.1370.3771.301100
3.02-3.157.50.26827620.9730.1050.2891.401100
3.15-3.327.50.16627600.9890.0650.1781.529100
3.32-3.537.50.10527660.9950.0410.1131.578100
3.53-3.87.40.06627820.9980.0260.0711.424100
3.8-4.187.40.05127810.9980.020.0551.709100
4.18-4.7870.04228200.9990.0170.0452.12399.7
4.78-6.017.30.03328170.9990.0130.0351.516100
6.01-256.70.021293910.0090.0231.09299.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNS1.2refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CUV

5cuv


Resolution: 2.8→25 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2326 1309 4.7 %
Rwork0.1984 25619 -
obs-26928 96.6 %
Solvent computationBsol: 48.8005 Å2
Displacement parametersBiso max: 137.87 Å2 / Biso mean: 60.285 Å2 / Biso min: 31.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.645 Å2-2.511 Å20 Å2
2--4.645 Å20 Å2
3----9.289 Å2
Refinement stepCycle: final / Resolution: 2.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 62 118 4434
Biso mean--104.38 59.02 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4971.5
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_mcangle_it2.6292
X-RAY DIFFRACTIONc_scangle_it3.3112.5
LS refinement shellResolution: 2.8→2.9 Å /
RfactorNum. reflection
Rfree0.329 -
Rwork0.284 2351
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2pop.par
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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