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- PDB-1qs7: The 1.8 angstrom structure of calmodulin rs20 peptide complex -

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Basic information

Entry
Database: PDB / ID: 1qs7
TitleThe 1.8 angstrom structure of calmodulin rs20 peptide complex
Components
  • CALMODULIN
  • RS20
KeywordsMETAL BINDING PROTEIN/PEPTIDE / CALMODULIN / CALCIUM BINDING / HELIX-LOOP-HELIX / SIGNALLING / COMPLEX(CALCIUM-BINDING PROTEIN-PEPTIDE) / METAL 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 / smooth muscle contraction / stress fiber / lamellipodium / calmodulin binding / protein kinase activity / phosphorylation ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cleavage furrow / smooth muscle contraction / stress fiber / lamellipodium / calmodulin binding / protein kinase activity / phosphorylation / calcium ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
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 / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / 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 / 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
: / EF-hand domain-containing protein / Myosin light chain kinase, smooth muscle / Myosin light chain kinase, smooth muscle
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeigand, S. / Anderson, W.F.
Citation
Journal: To be Published
Title: High Resolution Structure of a Calmodulin Rs20 Peptide Complex
Authors: Weigand, S. / Shuvalova, L. / Lukas, T.J. / Mirzoeva, S. / Watterson, D.M. / Anderson, W.F.
#1: 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.
#2: 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
DepositionJun 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
B: RS20
C: CALMODULIN
D: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,63212
Polymers37,3114
Non-polymers3218
Water4,756264
1
A: CALMODULIN
B: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8166
Polymers18,6562
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-72 kcal/mol
Surface area8600 Å2
MethodPISA
2
C: CALMODULIN
D: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8166
Polymers18,6562
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-62 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.016, 54.481, 66.304
Angle α, β, γ (deg.)90.00, 92.759, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CALMODULIN /


Mass: 16327.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: Synthetic Construct / Plasmid: PVUCH-1 / Production host: Escherichia coli (E. coli) / Strain (production host): UT481 / References: GenBank: 208092, UniProt: A0MMD0*PLUS
#2: Protein/peptide RS20


Mass: 2327.696 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PEPTIDE ANALOG OF THE CALMODULIN RECOGNITION REGION OF CHICKEN SMOOTH MUSCLE/ NONMUSCLE MYOSIN LIGHT CHAIN KINASE
References: UniProt: P19038, UniProt: P11799*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PRESENCE OR ABSENCE OF THE FORMYL BLOCKING GROUP ON TRYPTOPHAN-4 OF THE PEPTIDE HAS NO EFFECT ...THE PRESENCE OR ABSENCE OF THE FORMYL BLOCKING GROUP ON TRYPTOPHAN-4 OF THE PEPTIDE HAS NO EFFECT ON THE CALCIUM BINDING PROPERTIES OF THE WILD-TYPE CALMODULIN. (UNPUBLISHED)

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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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% (W/V) PEG 8000, 50 MM SODIUM ACETATE 5 MM CALCIUM CHLORIDE 0.01% (W/V) SODIUM AZIDE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 7, 1995 / Details: COLLIMATOR
RadiationMonochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→28.87 Å / Num. all: 39297 / Num. obs: 32557 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24
Reflection shellResolution: 1.59→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.6 / % possible all: 91.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VRK

1vrk


Resolution: 1.8→28.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1057648.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: ENGH, R.A. AND HUBER, R. (1991). ACTA CRYST. A47, 392-400.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2493 9.7 %RANDOM
Rwork0.228 ---
obs0.228 25684 94.4 %-
all-27212 --
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-6.86 Å20 Å20.6 Å2
2---1.66 Å20 Å2
3----5.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 8 264 2859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.342
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.408 167 9.4 %
Rwork0.373 1608 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MYCNSLIB:PROTEIN.PARAMMYCNSLIB:PROTEIN.TOP
X-RAY DIFFRACTION2MYCNSLIB:ION.PARAMWATER.TOP
X-RAY DIFFRACTION3MYCNSLIB:WATER.PARAMMYCNSLIB:NFW.TOP
X-RAY DIFFRACTION4MYCNSLIB:PATCHES.PARAMION.TOP
X-RAY DIFFRACTION5MYCNSLIB:NFW.PARAM

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