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- PDB-2f2o: Structure of calmodulin bound to a calcineurin peptide: a new way... -

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Basic information

Entry
Database: PDB / ID: 2f2o
TitleStructure of calmodulin bound to a calcineurin peptide: a new way of making an old binding mode
ComponentsCalmodulin fused with calmodulin-binding domain of calcineurin
KeywordsMETAL BINDING PROTEIN / EF-hands / calcium / calmodulin / calcineurin
Function / homology
Function and homology information


CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / FCERI mediated Ca+2 mobilization / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of signaling / positive regulation of saliva secretion / calmodulin-dependent protein phosphatase activity / calcineurin complex / renal filtration ...CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / FCERI mediated Ca+2 mobilization / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of signaling / positive regulation of saliva secretion / calmodulin-dependent protein phosphatase activity / calcineurin complex / renal filtration / calcineurin-NFAT signaling cascade / positive regulation of osteoclast differentiation / Ca2+ pathway / dephosphorylation / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of activated T cell proliferation / negative regulation of ryanodine-sensitive calcium-release channel activity / epidermis development / positive regulation of osteoblast differentiation / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / keratinocyte differentiation / protein dephosphorylation / modulation of chemical synaptic transmission / sarcolemma / Z disc / spindle pole / response to calcium ion / dendritic spine / calmodulin binding / protein domain specific binding / calcium ion binding / protein-containing complex / metal ion binding / cytosol / cytoplasm
Similarity search - Function
PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / : / EF-hand ...PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / : / 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
Calmodulin / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsYe, Q. / Wong, A. / Jia, Z.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of calmodulin bound to a calcineurin Peptide: a new way of making an old binding mode.
Authors: Ye, Q. / Li, X. / Wong, A. / Wei, Q. / Jia, Z.
History
DepositionNov 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 23, 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_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.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.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_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 fused with calmodulin-binding domain of calcineurin
B: Calmodulin fused with calmodulin-binding domain of calcineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,17110
Polymers39,8512
Non-polymers3218
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-124 kcal/mol
Surface area17250 Å2
MethodPISA
2
A: Calmodulin fused with calmodulin-binding domain of calcineurin
B: Calmodulin fused with calmodulin-binding domain of calcineurin
hetero molecules

A: Calmodulin fused with calmodulin-binding domain of calcineurin
B: Calmodulin fused with calmodulin-binding domain of calcineurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,34220
Polymers79,7014
Non-polymers64116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10430 Å2
ΔGint-268 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.237, 42.769, 71.150
Angle α, β, γ (deg.)90.00, 110.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin fused with calmodulin-binding domain of calcineurin


Mass: 19925.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P62157, UniProt: Q309F2
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.17→67.42 Å / Num. obs: 18574 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.057

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F2P

2f2p


Resolution: 2.17→67.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.886 / SU B: 7.38 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28856 1774 9.9 %RANDOM
Rwork0.20351 ---
all0.21235 16200 --
obs0.21235 16200 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.615 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.86 Å2
2--1.2 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.17→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 8 178 2676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0480.0222516
X-RAY DIFFRACTIONr_bond_other_d0.0030.022254
X-RAY DIFFRACTIONr_angle_refined_deg3.0651.963363
X-RAY DIFFRACTIONr_angle_other_deg1.34435260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5045309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1840.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022828
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
X-RAY DIFFRACTIONr_nbd_refined0.2830.2854
X-RAY DIFFRACTIONr_nbd_other0.270.22940
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1160.21490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.230
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7311.51554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.84822486
X-RAY DIFFRACTIONr_scbond_it4.8583962
X-RAY DIFFRACTIONr_scangle_it7.1224.5877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.172→2.228 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 125
Rwork0.196 1106

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