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- PDB-2ccm: X-ray structure of Calexcitin from Loligo pealeii at 1.8A -

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Basic information

Entry
Database: PDB / ID: 2ccm
TitleX-ray structure of Calexcitin from Loligo pealeii at 1.8A
ComponentsCALEXCITIN
KeywordsSIGNALING PROTEIN / EF HAND / CALCIUM
Function / homologyEF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha / metal ion binding / Calexcitin
Function and homology information
Biological speciesLOLIGO PEALEII (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsErskine, P.T. / Beaven, G.D.E. / Wood, S.P. / Fox, G. / Vernon, J. / Giese, K.P. / Cooper, J.B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the Neuronal Protein Calexcitin Suggests a Mode of Interaction in Signalling Pathways of Learning and Memory.
Authors: Erskine, P.T. / Beaven, G.D.E. / Hagan, R. / Findlow, I.S. / Werner, J.M. / Wood, S.P. / Vernon, J. / Giese, K.P. / Fox, G. / Cooper, J.B.
History
DepositionJan 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALEXCITIN
B: CALEXCITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8438
Polymers44,6022
Non-polymers2406
Water12,286682
1
A: CALEXCITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4214
Polymers22,3011
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALEXCITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4214
Polymers22,3011
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.635, 69.222, 134.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CALEXCITIN


Mass: 22301.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LOLIGO PEALEII (squid) / Tissue: OPTIC LOBE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76764
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.04 Å3/Da / Density % sol: 39.2 % / Description: SELENO-METHIONINE MAD
Crystal growpH: 5.5
Details: 30% PEG 4K, 0.2 M AMMONIUM ACETATE WITH 0.1 M SODIUM CITRATE AT PH 5.0 - 6.5 AND [PROTEIN]= 3 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→48.3 Å / Num. obs: 40926 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 25.992 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
MLPHAREphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→48.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 2026 4.9 %IN SHELLS
Rwork0.1906 ---
obs0.1906 40860 98.9 %-
Solvent computationSolvent model: CNS
Displacement parametersBiso mean: 34.242 Å2
Refine analyzeLuzzati d res low obs: 48.3 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 6 682 3805
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.924
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.6181.5
X-RAY DIFFRACTIONc_mcangle_it2.5832
X-RAY DIFFRACTIONc_scbond_it2.4022
X-RAY DIFFRACTIONc_scangle_it3.7912.5
LS refinement shellResolution: 1.8→1.82 Å / Total num. of bins used: 40 /
RfactorNum. reflection
Rwork0.3646 979

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