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- PDB-5cuy: Crystal structure of Trypanosoma brucei Vacuolar Soluble Pyrophos... -

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Basic information

Entry
Database: PDB / ID: 5cuy
TitleCrystal structure of Trypanosoma brucei Vacuolar Soluble Pyrophosphatases in apo form
ComponentsAcidocalcisomal pyrophosphatase
KeywordsMETAL BINDING PROTEIN / substrate binding / acidocalcisomal pyrophosphatase
Function / homology
Function and homology information


acidocalcisome / pyrophosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / calcium ion binding / magnesium ion binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / EF-hand domain pair
Similarity search - Domain/homology
CITRIC ACID / Inorganic diphosphatase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, Y.Y. / Ko, T.P. / 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
Revision 1.1Nov 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_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)190,48012
Polymers189,6154
Non-polymers8668
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28890 Å2
ΔGint-173 kcal/mol
Surface area67050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.917, 70.137, 141.759
Angle α, β, γ (deg.)90.00, 106.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Acidocalcisomal pyrophosphatase


Mass: 47403.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.02.4930 / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q384W3
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: potassium citrate tribasic,PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 64763 / % possible obs: 98.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Χ2: 1.185 / Net I/av σ(I): 15.394 / Net I/σ(I): 9.6 / Num. measured all: 216422
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.10.38361910.8960.2490.4580.72794.7
2.59-2.693.20.34163280.9110.2180.4060.82897.9
2.69-2.823.30.26864170.9450.1710.3190.86998.9
2.82-2.963.40.21265180.9610.1340.251199.7
2.96-3.153.40.15665080.9780.0980.1851.13899.7
3.15-3.393.50.11464990.9850.0720.1361.55799.6
3.39-3.733.50.0965420.9880.0570.1071.33599.6
3.73-4.273.40.07665500.990.0490.0911.50199.7
4.27-5.373.30.06965550.9910.0440.0821.5599.2
5.37-253.30.05766550.9940.0370.0681.22498.7

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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: 2.5→25 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2515 3114 4.8 %
Rwork0.1941 58607 -
obs-61721 94.2 %
Solvent computationBsol: 28.9844 Å2
Displacement parametersBiso max: 121.04 Å2 / Biso mean: 50.4658 Å2 / Biso min: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1-17.724 Å20 Å2-0.009 Å2
2---27.258 Å20 Å2
3---9.534 Å2
Refinement stepCycle: final / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12632 0 56 686 13374
Biso mean--99.96 49.63 -
Num. residues----1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5961.5
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_mcangle_it2.8012
X-RAY DIFFRACTIONc_scangle_it3.0652.5
LS refinement shellResolution: 2.5→2.59 Å /
RfactorNum. reflection
Rfree0.353 -
Rwork0.327 5068
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4cit.par

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