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- PDB-1vrk: THE 1.9 ANGSTROM STRUCTURE OF E84K-CALMODULIN RS20 PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1vrk
TitleTHE 1.9 ANGSTROM STRUCTURE OF E84K-CALMODULIN RS20 PEPTIDE COMPLEX
Components
  • CALMODULIN
  • RS20
KeywordsCOMPLEX(CALCIUM-BINDING PROTEIN/PEPTIDE) / CALMODULIN / CALCIUM BINDING / HELIX-LOOP-HELIX / SIGNALLING / COMPLEX(CALCIUM-BINDING PROTEIN-PEPTIDE) / COMPLEX(CALCIUM-BINDING PROTEIN-PEPTIDE) complex
Function / homology
Function and homology information


tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cleavage furrow / stress fiber / lamellipodium / calmodulin binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / Myosin light chain kinase, smooth muscle
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWeigand, S. / Anderson, W.F.
Citation
Journal: Biochemistry / Year: 1999
Title: Analysis of the functional coupling between calmodulin's calcium binding and peptide recognition properties.
Authors: Mirzoeva, S. / Weigand, S. / Lukas, T.J. / Shuvalova, L. / Anderson, W.F. / Watterson, D.M.
#1: 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.
History
DepositionSep 24, 1997Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 650HELIX THE STRUCTURAL CONSEQUENCE OF THE E84K MUTATION RELATIVE TO THE WILD TYPE STRUCTURE ...HELIX THE STRUCTURAL CONSEQUENCE OF THE E84K MUTATION RELATIVE TO THE WILD TYPE STRUCTURE (REFERENCE 1 ABOVE) IS AN ALTERATION OF THE RESIDUE 84 CONFORMATION AND A FIVE DEGREE MOVEMENT OF HELIX E (HELIX 5) AWAY FROM THE PEPTIDE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALMODULIN
B: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1897
Polymers18,9702
Non-polymers2195
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-75 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.209, 40.560, 32.774
Angle α, β, γ (deg.)90.00, 91.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CALMODULIN


Mass: 16642.338 Da / Num. of mol.: 1 / Mutation: E84K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Description: CONSENSUS SEQUENCE FROM A NUMBER OF SOURCES; / Plasmid: PVUCH-1 / Production host: Escherichia coli (E. coli) / Strain (production host): UT481 / References: GenBank: 3561059
#2: Protein/peptide RS20


Mass: 2327.696 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TRP 4 IS NE-FORMYLATED / References: UniProt: P11799*PLUS, EC: 2.7.1.117
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#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.: 141 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ENHANCEMENT OF CALMODULIN'S CALCIUM BINDING BY SMOOTH MUSCLE/NONMUSCLE MYOSIN LIGHT CHAIN ...THE ENHANCEMENT OF CALMODULIN'S CALCIUM BINDING BY SMOOTH MUSCLE/NONMUSCLE MYOSIN LIGHT CHAIN KINASE OR THE RS20 PEPTIDE ANALOG (CHAIN B) IS DIMINISHED BY THE MUTATION OF GLUTAMATE-84 TO LYSINE (E84K). THE PRESENCE OR ABSENCE OF THE FORMYL BLOCKING GROUP ON TRYPTOPHAN-4 OF THE PEPTIDE HAS NO EFFECT ON THE CALCIUM BINDING PROPERTIES OF EITHER THE WILD-TYPE OR E84K MUTANT CALMODULIN. (UNPUBLISHED)
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 43 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.6 mg/mlE84K-CaM1drop
210 mMTris-HCl1drop
33 mg/mlpeptide1drop
44 %PEG80001drop
520 mMsodium acetate1drop
61 mM1dropCaCl2
70.002 %sodium azide1drop
820 %PEG80001reservoir
9100 mMsodium acetate1reservoir
105 mM1reservoirCaCl2
110.01 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1993 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→18.2 Å / Num. obs: 11190 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.0649 / Net I/σ(I): 15
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2 / % possible all: 65

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDL: SECOND COMPLEX (SEGID B AND F) OF THE ASYMMETRIC UNIT

1cdl


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1029 10.3 %RANDOM
Rwork0.171 ---
obs0.171 10032 78 %-
Displacement parametersBiso mean: 30.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 8 141 1492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.981.5
X-RAY DIFFRACTIONx_mcangle_it5.562
X-RAY DIFFRACTIONx_scbond_it6.92
X-RAY DIFFRACTIONx_scangle_it9.642.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 86 9.7 %
Rwork0.256 805 -
obs--41.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSCALCIUM.TOP
X-RAY DIFFRACTION3WAT_ACT_FOR.PARWAT_ACT_FOR.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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