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

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Basic information

Entry
Database: PDB / ID: 5cuv
TitleCrystal structure of Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in apo form
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 / nucleus / cytoplasm
Similarity search - Function
Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / EF-hand domain pair
Similarity search - Domain/homology
D-MALATE / inorganic diphosphatase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.62 Å
AuthorsKo, T.P. / Yang, Y.Y. / Liu, W.D. / 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

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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)97,8885
Polymers97,7062
Non-polymers1833
Water6,233346
1
A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules

A: Acidocalcisomal pyrophosphatase
B: Acidocalcisomal pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,77710
Polymers195,4114
Non-polymers3656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area24270 Å2
ΔGint-169 kcal/mol
Surface area66790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.518, 103.017, 157.398
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: 48852.785 Da / Num. of mol.: 2
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.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.29 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: DL-malic acid, PEG3350, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9790, 0.9791, 0.9639
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2014
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.9791
30.97911
40.96391
ReflectionResolution: 2.62→25 Å / Num. obs: 24891 / % possible obs: 99.9 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.034 / Rrim(I) all: 0.115 / Χ2: 1.643 / Net I/av σ(I): 26.685 / Net I/σ(I): 12.1 / Num. measured all: 280552
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.7111.50.50724670.9530.1560.5311.077100
2.71-2.8211.50.40624280.9590.1240.4251.122100
2.82-2.9511.50.28324790.980.0870.2961.27100
2.95-3.1111.50.21124650.9890.0650.2211.295100
3.11-3.311.50.15124510.9940.0460.1581.318100
3.3-3.5511.40.10624860.9960.0330.1111.374100
3.55-3.9111.20.0924610.9970.0280.0951.262100
3.91-4.4711.10.07825150.9980.0240.0821.571100
4.47-5.6310.60.06925210.9980.0220.0731.96799.8
5.63-2510.90.07926180.9980.0240.0824.17799.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
CNS1.21refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.62→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1167 4.7 %Random
Rwork0.1775 23085 --
obs-23085 97.4 %-
Solvent computationBsol: 48.4499 Å2
Displacement parametersBiso max: 144.38 Å2 / Biso mean: 44.9438 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.964 Å2-0 Å20 Å2
2--4.709 Å20 Å2
3----6.673 Å2
Refinement stepCycle: LAST / Resolution: 2.62→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 11 347 6579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5591.5
X-RAY DIFFRACTIONc_scbond_it2.0572
X-RAY DIFFRACTIONc_mcangle_it2.7252
X-RAY DIFFRACTIONc_scangle_it3.1712.5
LS refinement shellResolution: 2.62→2.71 Å /
RfactorNum. reflection
Rfree0.311 -
Rwork0.262 2136
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4mlt_xplor.par

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