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- PDB-1omr: non-myristoylated wild-type bovine recoverin with calcium bound t... -

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Basic information

Entry
Database: PDB / ID: 1omr
Titlenon-myristoylated wild-type bovine recoverin with calcium bound to EF-hand 3
Componentsrecoverin
KeywordsMETAL BINDING PROTEIN / EF-hand / helix-loop-helix
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: 1.5 Å
AuthorsWeiergraber, O.H. / Granzin, J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Impact of N-terminal myristoylation on the Ca2+-dependent conformational transition in recoverin
Authors: Weiergraber, O.H. / Senin, I.I. / Philippov, P.P. / Granzin, J. / Koch, K.-W.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2752
Polymers23,2351
Non-polymers401
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: recoverin
hetero molecules

A: recoverin
hetero molecules

A: recoverin
hetero molecules

A: recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1018
Polymers92,9414
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area9410 Å2
ΔGint-110 kcal/mol
Surface area33710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.051, 84.051, 59.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein recoverin /


Mass: 23235.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: RCV1 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): rec/BL21 / References: UniProt: P21457
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.16 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, TRIS, calcium chloride, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1droppH8.0
21 mM1dropCaCl2
31 mM1dropMgCl2
470-80 %satammonium sulfate1reservoir

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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: Apr 21, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→48.39 Å / Num. all: 33042 / Num. obs: 33042 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 5.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / Num. unique all: 2444 / Rsym value: 0.36 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.422

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1REC

1rec


Resolution: 1.5→48.39 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1650 -random
Rwork0.249 ---
obs0.249 33042 99.7 %-
all-33042 --
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.5→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 1 85 1725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.5→1.52 Å / Rfactor Rfree error: 0.058
RfactorNum. reflection% reflection
Rfree0.391 46 -
Rwork0.33 --
obs-1009 100 %
Refinement
*PLUS
Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.329
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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