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- PDB-1ooj: Structural genomics of Caenorhabditis elegans : Calmodulin -

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Basic information

Entry
Database: PDB / ID: 1ooj
TitleStructural genomics of Caenorhabditis elegans : Calmodulin
ComponentsCalmodulin CMD-1
KeywordsMETAL BINDING PROTEIN / Structural genomics / Calmodulin / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


establishment of meiotic spindle orientation / calcineurin complex / embryo development ending in birth or egg hatching / apoptotic cell clearance / positive chemotaxis / enzyme regulator activity / cell periphery / microtubule cytoskeleton organization / mitotic spindle / cell migration ...establishment of meiotic spindle orientation / calcineurin complex / embryo development ending in birth or egg hatching / apoptotic cell clearance / positive chemotaxis / enzyme regulator activity / cell periphery / microtubule cytoskeleton organization / mitotic spindle / cell migration / regulation of protein localization / nuclear membrane / regulation of apoptotic process / regulation of cell cycle / negative regulation of gene expression / calcium ion binding / centrosome / 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 speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSymersky, J. / Lin, G. / Li, S. / Qiu, S. / Luan, C.-H. / Luo, D. / Tsao, J. / Carson, M. / DeLucas, L. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Proteins / Year: 2003
Title: Structural genomics of caenorhabditis elegans: crystal structure of calmodulin.
Authors: Symersky, J. / Lin, G. / Li, S. / Qiu, S. / Carson, M. / Schormann, N. / Luo, M.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin CMD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0005
Polymers16,8401
Non-polymers1604
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.394, 23.997, 60.770
Angle α, β, γ (deg.)90.00, 112.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin CMD-1


Mass: 16839.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pDEST 17.1 / Production host: Escherichia coli (E. coli) / References: UniProt: O16305
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.07 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K, RESERVOIR: MPD, PEG3350, DIOXANE, 5 MM CACL2, 50 MM CITRATE, PH 5.7, PROTEIN STOCK: 5 MG/ML IN 5 MM CACL2, 5 MM CACODYLATE, PH 6, ...Details: PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.0K, RESERVOIR: MPD, PEG3350, DIOXANE, 5 MM CACL2, 50 MM CITRATE, PH 5.7, PROTEIN STOCK: 5 MG/ML IN 5 MM CACL2, 5 MM CACODYLATE, PH 6, DROPS: 5 MICROLITERS OF PROTEIN STOCK SOLUTION, 5 MICROLITERS OF RESERVOIR.
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mMisopropanol1drop
25 mM1dropCaCl2
35 mMsodium cacodylate1droppH6.
45 mg/mlprotein1drop
550 %(v/v)MPD1reservoir
645 %(w/v)PEG33501reservoir
712 %(v/v)dioxane1reservoir
85 mM1reservoirCaCl2
950 mMsodium citrate1reservoirpH5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.107 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.107 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 8241 / Num. obs: 8241 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.071 / Net I/σ(I): 12
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 9.3 / Num. unique all: 839 / Rsym value: 0.202 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 29757 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.202

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Processing

Software
NameVersionClassification
HKL-2000data reduction
AMoREphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CLN

4cln


Resolution: 2.11→30 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 410 5.4 %RANDOM
Rwork0.212 ---
obs0.223 7530 90.7 %-
all-8025 --
Solvent computationSolvent model: flat model / Bsol: 68.53 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.11→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 4 91 1206
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.121
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.11→2.19 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 38 6.2 %
Rwork0.287 575 -
obs-764 73.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.38

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