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- PDB-3w56: Structure of a C2 domain -

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Basic information

Entry
Database: PDB / ID: 3w56
TitleStructure of a C2 domain
ComponentsC2 domain protein
KeywordsLIPID BINDING PROTEIN / C2 domain
Function / homology
Function and homology information


immunological synapse formation / wide pore channel activity / T cell mediated cytotoxicity / defense response to virus / metal ion binding / membrane
Similarity search - Function
: / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesScophthalmus maximus (turbot)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTraore, D.A.K. / Whisstock, J.C.
CitationJournal: Biochem.J. / Year: 2013
Title: Defining the interaction of perforin with calcium and the phospholipid membrane.
Authors: Traore, D.A. / Brennan, A.J. / Law, R.H. / Dogovski, C. / Perugini, M.A. / Lukoyanova, N. / Leung, E.W. / Norton, R.S. / Lopez, J.A. / Browne, K.A. / Yagita, H. / Lloyd, G.J. / Ciccone, A. / ...Authors: Traore, D.A. / Brennan, A.J. / Law, R.H. / Dogovski, C. / Perugini, M.A. / Lukoyanova, N. / Leung, E.W. / Norton, R.S. / Lopez, J.A. / Browne, K.A. / Yagita, H. / Lloyd, G.J. / Ciccone, A. / Verschoor, S. / Trapani, J.A. / Whisstock, J.C. / Voskoboinik, I.
History
DepositionJan 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C2 domain protein


Theoretical massNumber of molelcules
Total (without water)15,2901
Polymers15,2901
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.348, 55.219, 89.746
Angle α, β, γ (deg.)90.000, 91.170, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-212-

HOH

21A-216-

HOH

31A-328-

HOH

41A-347-

HOH

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Components

#1: Protein C2 domain protein / SmC2P1


Mass: 15289.983 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scophthalmus maximus (turbot) / Gene: C2P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle / References: UniProt: E2FYL5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.1 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 100mM Tris-HCl, 200mM MgCl2, 20% PEG 3350, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953697 Å / Relative weight: 1
ReflectionResolution: 1.6→47.027 Å / Num. all: 16003 / Num. obs: 16003 / % possible obs: 97.9 % / Redundancy: 4.6 % / Rsym value: 0.077 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.694.60.3990.35521054822920.1820.3990.3552.396.5
1.69-1.794.60.2690.2392.9993221630.1220.2690.2393.296.9
1.79-1.914.60.2780.2462.2928820390.1290.2780.2464.697.2
1.91-2.074.50.1850.1643.5881419380.0850.1850.1647.197.8
2.07-2.264.50.170.153.3807917990.0790.170.158.998.2
2.26-2.534.60.0880.0787741216100.040.0880.07810.398.3
2.53-2.924.60.0680.0619.8658114270.0310.0680.06114.199
2.92-3.584.60.0610.0548.3567012450.0280.0610.05418.999.3
3.58-5.064.50.050.04512.442859550.0230.050.04522.399.7
5.06-44.8644.50.0540.04810.424075350.0250.0540.04821.199.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIXdev_895refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NSJ

3nsj


Resolution: 1.6→27.61 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.22 / σ(F): 0 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 815 5.14 %
Rwork0.2116 --
obs0.2137 15867 96.85 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.217 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 71.6 Å2 / Biso mean: 22.5196 Å2 / Biso min: 5.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.8551 Å20 Å2-2.2395 Å2
2--5.9401 Å20 Å2
3----4.085 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 0 152 1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019905
X-RAY DIFFRACTIONf_angle_d1.8531223
X-RAY DIFFRACTIONf_chiral_restr0.129130
X-RAY DIFFRACTIONf_plane_restr0.009159
X-RAY DIFFRACTIONf_dihedral_angle_d15.456322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6001-1.70030.31221440.27042464260896
1.7003-1.83160.2961560.23982452260897
1.8316-2.01590.33371250.28442475260096
2.0159-2.30740.34881220.25112479260195
2.3074-2.90660.24261290.21012558268798
2.9066-27.61370.18511390.16652624276399

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