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- PDB-1qtx: THE 1.65 ANGSTROM STRUCTURE OF CALMODULIN RS20 PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qtx
TitleTHE 1.65 ANGSTROM STRUCTURE OF CALMODULIN RS20 PEPTIDE COMPLEX
Components
  • PROTEIN (CALMODULIN)
  • PROTEIN (RS20)
KeywordsSIGNALING PROTEIN / CALMODULIN / CALCIUM BINDING / HELIX-LOOP-HELIX / SIGNALING / COMPLEX (CALCIUM- BINDING PROTEIN-PEPTIDE)
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 / phosphorylation / calcium ion binding / ATP binding ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / cleavage furrow / stress fiber / lamellipodium / calmodulin binding / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 29, 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 1.3Aug 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_conn_type / 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.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_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: PROTEIN (CALMODULIN)
B: PROTEIN (RS20)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1026
Polymers18,9422
Non-polymers1604
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-70 kcal/mol
Surface area9090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.046, 55.344, 41.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (CALMODULIN)


Mass: 16642.271 Da / Num. of mol.: 1
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 PROTEIN (RS20)


Mass: 2299.686 Da / Num. of mol.: 1
Fragment: CALMODULIN BINDING REGION FROM SMOOTH MUSCLE/NONMUSCLE MYOSIN LIGHT CHAIN KINASE
Source method: obtained synthetically
Details: PEPTIDE ANALOG OF THE CALMODULIN RECOGNITION REGION OF CHICKEN SMOOTH MUSCLE/ NONMUSCLE MYOSIN LIGHT CHAIN KINASE
References: UniProt: P11799
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% (W/V) PEG 8000, 100 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

Diffraction
IDMean temperature (K)Crystal-ID
1951
2961
3921
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEJan 8, 1996COLLIMATOR
RIGAKU RAXIS IIC2IMAGE PLATEFeb 9, 1996
RIGAKU RAXIS IIC3IMAGE PLATEFeb 28, 1996
RadiationMonochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. all: 166836 / Num. obs: 19966 / % possible obs: 79.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.9 / % possible all: 59.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VRM CHAIN A AND CHAIN B

1vrm


Resolution: 1.65→29.595 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1176942.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
Stereochemistry target values: ENGH, R.A. AND HUBER, R. (1991). ACTA CRYST. A47, 392-400.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1801 10.3 %RANDOM
Rwork0.185 ---
all0.185 17495 --
obs0.185 17495 87.3 %-
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.65→29.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 8 324 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.552.5
LS refinement shellResolution: 1.65→1.69 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.249 82 10.9 %
Rwork0.237 671 -
obs--60.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAMYCNSLIB:PROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAION.TOP
X-RAY DIFFRACTION4MYCNSLIB:PATCHES.PARAM

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