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- PDB-1prw: Crystal structure of bovine brain Ca++ calmodulin in a compact form -

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Basic information

Entry
Database: PDB / ID: 1prw
TitleCrystal structure of bovine brain Ca++ calmodulin in a compact form
ComponentsCalmodulin
KeywordsMETAL BINDING PROTEIN / EF HAND / CALCIUM-BINDING PROTEIN / KINASE ACTIVATOR
Function / homology
Function and homology information


regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / spindle pole / myelin sheath / protein domain specific binding / calcium ion binding / centrosome / protein-containing complex / cytoplasm / cytosol
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRSAS / Resolution: 1.7 Å
AuthorsFallon, J.L. / Quiocho, F.A.
Citation
Journal: Structure / Year: 2003
Title: A closed compact structure of native ca(2+)-calmodulin.
Authors: Fallon, J.L. / Quiocho, F.A.
#1: Journal: Nat.Struct.Biol. / Year: 2002
Title: Man bites dog
Authors: Meador, W.E. / Quiocho, F.A.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: X-ray analysis reveals conformational adaptation of the linker in functional calmodulin mutants
Authors: Meador, W.E. / George, S.E. / Means, A.R. / Quiocho, F.A.
#3: Journal: Science / Year: 1993
Title: Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
#4: Journal: Science / Year: 1992
Title: Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
#5: Journal: J.Mol.Biol. / Year: 1992
Title: Calmodulin structure refined at 1.7 A resolution
Authors: Chattopadhyaya, R. / Meador, W.E. / Means, A.R. / Quiocho, F.A.
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9505
Polymers16,7891
Non-polymers1604
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.320, 35.750, 68.030
Angle α, β, γ (deg.)90.00, 117.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin


Mass: 16789.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P62157
#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.: 172 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 6000, sodium acetate, glycerol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1dropCaCl2
210 mg/mlprotein1drop
340 %PEG60001reservoir
450 mMsodium acetate1reservoir
510 mM1reservoirCaCl2pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→14 Å / Num. all: 15132 / Num. obs: 13383 / % possible obs: 88.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.28 / Num. unique all: 1377 / Rsym value: 0.42 / % possible all: 90.7
Reflection
*PLUS
Num. obs: 12598 / % possible obs: 92.4 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 90.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: SIRSAS / Resolution: 1.7→14.59 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 533665.65 / Data cutoff high rms absF: 533665.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: The atoms CE, NZ of Lys13 and CD, CE, NZ of Lys21 are present in the file even though the electron density for these atoms is missing
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1280 10.2 %RANDOM
Rwork0.186 ---
all0.186 15132 --
obs0.186 12598 83.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.7254 Å2 / ksol: 0.462227 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20.22 Å2
2---1.32 Å20 Å2
3---0.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 4 172 1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.362.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 188 11.1 %
Rwork0.226 1505 -
obs-1377 67.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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