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- PDB-1n0y: Crystal Structure of Pb-bound Calmodulin -

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Basic information

Entry
Database: PDB / ID: 1n0y
TitleCrystal Structure of Pb-bound Calmodulin
ComponentsCalmodulin
KeywordsMETAL BINDING PROTEIN / calmodulin / lead
Function / homology
Function and homology information


enzyme regulator activity / calcium ion binding
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / LEAD (II) ION / Calmodulin
Similarity search - Component
Biological speciesParamecium tetraurelia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsWilson, M.A. / Brunger, A.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Domain flexibility in the 1.75 A resolution structure of Pb2+-calmodulin.
Authors: Wilson, M.A. / Brunger, A.T.
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,47218
Polymers33,3752
Non-polymers3,09716
Water2,684149
1
A: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2759
Polymers16,6871
Non-polymers1,5878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1979
Polymers16,6871
Non-polymers1,5098
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.936, 30.792, 113.084
Angle α, β, γ (deg.)90.00, 109.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin


Mass: 16687.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Gene: CAM / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P07463
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: MPD, sodium cacodylate, sodium acetate, lead nitrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160-65 %MPD1reservoir
250 mMsodium cacodylate1reservoirpH5.0
315 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.946 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 2000
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 1.75→53 Å / Num. all: 33765 / Num. obs: 33157 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3174 / % possible all: 94.7
Reflection
*PLUS
Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→53 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.906 / SU B: 1.653 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 3312 10 %RANDOM
Rwork0.21344 ---
all0.21437 33594 --
obs0.21437 33157 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.71 Å2
2---0.94 Å20 Å2
3---1.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 1.75→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 23 149 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211331
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9821781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.7555164
X-RAY DIFFRACTIONr_chiral_restr0.0750.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021011
X-RAY DIFFRACTIONr_nbd_refined0.2720.2711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.214
X-RAY DIFFRACTIONr_mcbond_it0.5441.5824
X-RAY DIFFRACTIONr_mcangle_it1.0921313
X-RAY DIFFRACTIONr_scbond_it2.3313507
X-RAY DIFFRACTIONr_scangle_it3.8254.5468
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 215 -
Rwork0.253 2112 -
obs-2327 94.7 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.219

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