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- PDB-2h2n: Crystal structure of human soluble calcium-activated nucleotidase... -

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Basic information

Entry
Database: PDB / ID: 2h2n
TitleCrystal structure of human soluble calcium-activated nucleotidase (SCAN) with calcium ion
ComponentsSoluble calcium-activated nucleotidase 1
KeywordsHYDROLASE / NUCLEOTIDASE / FIVE-BLADE BETA PROPELLER / CALCIUM-BINDING PROTEIN / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen ...nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Apyrase / Apyrase / Apyrase / Apyrase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Soluble calcium-activated nucleotidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, M. / Horii, K. / Herr, A.B. / Kirley, T.L.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Calcium-dependent dimerization of human soluble calcium activated nucleotidase: characterization of the dimer interface.
Authors: Yang, M. / Horii, K. / Herr, A.B. / Kirley, T.L.
History
DepositionMay 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble calcium-activated nucleotidase 1
B: Soluble calcium-activated nucleotidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7555
Polymers75,6162
Non-polymers1393
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.094, 52.368, 77.426
Angle α, β, γ (deg.)75.060, 74.520, 79.470
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a dimer (chains A and B) in the asymmetric unit.

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Components

#1: Protein Soluble calcium-activated nucleotidase 1 / SCAN-1 / Apyrase homolog / Putative NF-kappa-B-activating protein 107 / Putative MAPK-activating protein PM09


Mass: 37808.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CANT1, SHAPY / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q8WVQ1, nucleoside diphosphate phosphatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 8% PEG 4000, 0.2 M ammonium sulfate, 0.1M sodium acetate pH4.8, 10 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2005 / Details: OSMIC CONFOCAL MIRRORS
RadiationMonochromator: OSMIC CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→31.08 Å / Num. obs: 27727 / % possible obs: 99.7 % / Redundancy: 5.43 % / Rmerge(I) obs: 0.058 / Χ2: 0.9 / Net I/σ(I): 17.9 / Scaling rejects: 1641
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.3-2.385.130.1784.91446227990.4899.3
2.38-2.485.210.1585.41433027300.4699.3
2.48-2.595.250.1416.51456227570.5399.4
2.59-2.735.310.1277.21481127730.5499.7
2.73-2.95.430.1039.41529728040.6599.9
2.9-3.125.530.08512.51530927570.76100
3.12-3.435.630.06917.71565827690.92100
3.43-3.935.60.05326.11583027941.17100
3.93-4.955.620.03940.31592627651.6899.9
4.95-31.085.570.03645.21596727791.6699.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å31.08 Å
Translation2.5 Å31.08 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→31.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.05 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.259 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1395 5 %RANDOM
Rwork0.168 ---
all0.172 ---
obs0.172 27727 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.747 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 6 228 5232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0225127
X-RAY DIFFRACTIONr_angle_refined_deg2.1361.9466965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25224.139244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64815832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5521530
X-RAY DIFFRACTIONr_chiral_restr0.1440.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023964
X-RAY DIFFRACTIONr_nbd_refined0.2280.22111
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23374
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2279
X-RAY DIFFRACTIONr_metal_ion_refined0.070.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.210
X-RAY DIFFRACTIONr_mcbond_it1.2871.53229
X-RAY DIFFRACTIONr_mcangle_it2.14425040
X-RAY DIFFRACTIONr_scbond_it3.42332252
X-RAY DIFFRACTIONr_scangle_it5.1724.51925
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 91 -
Rwork0.216 1964 -
obs-2055 100 %

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