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- PDB-1exr: THE 1.0 ANGSTROM CRYSTAL STRUCTURE OF CA+2 BOUND CALMODULIN -

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Basic information

Entry
Database: PDB / ID: 1exr
TitleTHE 1.0 ANGSTROM CRYSTAL STRUCTURE OF CA+2 BOUND CALMODULIN
ComponentsCALMODULIN
KeywordsMETAL TRANSPORT / CALMODULIN / HIGH RESOLUTION / DISORDER
Function / homology
Function and homology information


enzyme regulator activity / calcium ion binding / cytoplasm
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesParamecium tetraurelia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsWilson, M.A. / Brunger, A.T.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The 1.0 A crystal structure of Ca(2+)-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity
Authors: Wilson, M.A. / Brunger, A.T.
History
DepositionMay 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8886
Polymers16,6871
Non-polymers2005
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.015, 29.415, 52.761
Angle α, β, γ (deg.)89.54, 86.10, 82.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CALMODULIN


Mass: 16687.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Plasmid: PKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P07463
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5
Details: MPD, calcium chloride, sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlCaM1drop
25 mM1dropCaCl2
350 mMsodium cacodylate1drop
550 mMsodium cacodylate1reservoir
650 %MPD1reservoir
4MPD1drop0.001ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.886
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 1999 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 78247 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.4
Reflection shellResolution: 1→1.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.1 / % possible all: 83.9
Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 5.4 %
Reflection shell
*PLUS
% possible obs: 83.9 % / Redundancy: 3.3 % / Num. unique obs: 6757 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED 1.1 A PARAMECIUM TETRAURELIA CALMODULIN

Resolution: 1→500 Å / Num. parameters: 14894 / Num. restraintsaints: 22732 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 9%
RfactorNum. reflection% reflectionSelection details
Rfree0.163 7782 10 %RANDOM
all0.136 77150 --
obs0.134 -96 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91 (1973)201-228
Refine analyzeNum. disordered residues: 36 / Occupancy sum hydrogen: 1089 / Occupancy sum non hydrogen: 1327
Refinement stepCycle: LAST / Resolution: 1→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 5 178 1650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.08
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.1
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor all: 0.1368 / Rfactor obs: 0.1345 / Rfactor Rwork: 0.134
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.023
X-RAY DIFFRACTIONs_chiral_restr0.07

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