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- PDB-2het: Non-myristoylated bovine recoverin (truncated at C-terminus) with... -

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Basic information

Entry
Database: PDB / ID: 2het
TitleNon-myristoylated bovine recoverin (truncated at C-terminus) with calcium bound to EF-hand 3
ComponentsRecoverin
KeywordsMETAL BINDING PROTEIN / Recoverin / EF-hand / helix-loop-helix / calcium binding
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / regulation of calcium ion transport / phototransduction / photoreceptor outer segment / photoreceptor inner segment / visual perception / perikaryon / calcium ion binding / membrane / cytosol
Similarity search - Function
Recoverin family / EF hand / EF-hand domain pair / 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. ...Recoverin family / EF hand / EF-hand domain pair / 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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWeiergraber, O.H. / Granzin, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Tuning of a neuronal calcium sensor.
Authors: Weiergraber, O.H. / Senin, I.I. / Zernii, E.Y. / Churumova, V.A. / Kovaleva, N.A. / Nazipova, A.A. / Permyakov, S.E. / Permyakov, E.A. / Philippov, P.P. / Granzin, J. / Koch, K.W.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_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_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_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_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: Recoverin
B: Recoverin
C: Recoverin
D: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1548
Polymers86,9934
Non-polymers1604
Water0
1
A: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7882
Polymers21,7481
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-91 kcal/mol
Surface area31080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.889, 70.759, 85.925
Angle α, β, γ (deg.)90.00, 99.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Recoverin / / p26


Mass: 21748.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RCV1 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21457
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M sodium malonate, 2 mM calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2006 / Details: Monochromators, mirrors
RadiationMonochromator: Diamond, germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→70 Å / Num. all: 14380 / Num. obs: 14380 / % possible obs: 84.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 89.4 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 11.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2072 / Rsym value: 0.234 / % possible all: 84.1

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Processing

Software
NameClassification
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMR

1omr


Resolution: 3→70 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 775 Shells
Rwork0.237 --
all0.238 14370 -
obs0.238 14370 -
Displacement parametersBiso mean: 77.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.64 Å20 Å24.03 Å2
2---8.18 Å20 Å2
3---18.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5756 0 4 0 5760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.81

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