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- PDB-5coc: Fusion protein of human calmodulin and B4 domain of protein A fro... -

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Basic information

Entry
Database: PDB / ID: 5coc
TitleFusion protein of human calmodulin and B4 domain of protein A from staphylococcal aureus
ComponentsImmunoglobulin G-binding protein A,Calmodulin
KeywordsPROTEIN BINDING / Fusion / alpha helix / cross-linker
Function / homology
Function and homology information


: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / IgG binding / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / IgG binding / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / response to corticosterone / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / mitochondrial membrane / positive regulation of protein serine/threonine kinase activity / spindle microtubule / synaptic vesicle membrane / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / 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
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Calmodulin-3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6691 Å
AuthorsJeong, W.H. / Lee, H. / Song, D.H. / Lee, J.O.
CitationJournal: Nat Commun / Year: 2016
Title: Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.
Authors: Jeong, W.H. / Lee, H. / Song, D.H. / Eom, J.H. / Kim, S.C. / Lee, H.S. / Lee, H. / Lee, J.O.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A,Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6303
Polymers14,5501
Non-polymers802
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.807, 98.807, 31.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Antibody Immunoglobulin G-binding protein A,Calmodulin / IgG-binding protein A / Staphylococcal protein A / CaM


Mass: 14550.117 Da / Num. of mol.: 1
Fragment: B4 domain (UNP RESIDUES 213-267),N-terminal (UNP RESIDUES 5-78)
Mutation: G240A, K261C, L1005A, T1006A, Q1009C
Source method: isolated from a genetically manipulated source
Details: The fusion protein of residues 213-267 from Immunoglobulin G-binding protein A and residues 5-78 of Calmodulin
Source: (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Homo sapiens (human)
Gene: spa, CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P38507, UniProt: P62158
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 10% w/v PEG 1000, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6691→50 Å / Num. obs: 4463 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.099 / Χ2: 1.641 / Net I/av σ(I): 22.74 / Net I/σ(I): 10.4 / Num. measured all: 26545
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6691-2.84.70.5764351.02799.5
2.8-2.915.30.4654451.111100
2.91-3.045.60.4954361.1799.8
3.04-3.25.80.3034441.2799.6
3.2-3.46.30.2274361.472100
3.4-3.666.40.1584511.71799.8
3.66-4.036.50.1144491.862100
4.03-4.626.50.0734441.984100
4.62-5.816.40.0674482.06100
5.81-505.90.0434752.27697.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2SPZ, 1CLL

2spz

1cll


Resolution: 2.6691→31.246 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 446 10 %
Rwork0.206 4014 -
obs0.2111 4460 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.16 Å2 / Biso mean: 65.4115 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.6691→31.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 2 12 978
Biso mean--51.33 20.83 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009977
X-RAY DIFFRACTIONf_angle_d1.1051315
X-RAY DIFFRACTIONf_chiral_restr0.04145
X-RAY DIFFRACTIONf_plane_restr0.005181
X-RAY DIFFRACTIONf_dihedral_angle_d17.527370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6691-3.0550.35821410.31691277141897
3.055-3.84790.30841480.242113511499100
3.8479-31.24760.21091570.16131386154399
Refinement TLS params.Method: refined / Origin x: -7.1043 Å / Origin y: -6.3182 Å / Origin z: 4.9416 Å
111213212223313233
T0.3512 Å2-0.0491 Å2-0.0504 Å2-0.3914 Å20.0136 Å2--0.4129 Å2
L0.221 °2-0.2264 °2-0.1371 °2-0.4533 °20.4019 °2--0.6936 °2
S0.0096 Å °0.0464 Å °-0.0074 Å °-0.0114 Å °0.0467 Å °0.0732 Å °-0.0114 Å °-0.0239 Å °0 Å °
Refinement TLS groupSelection details: chain A

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