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- PDB-4m2p: Crystal structure of a non-myristoylated C39D recoverin mutant wi... -

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Basic information

Entry
Database: PDB / ID: 4m2p
TitleCrystal structure of a non-myristoylated C39D recoverin mutant with one calcium ion bound to EF-hand 3
ComponentsRecoverin
KeywordsMETAL BINDING PROTEIN / CALCIUM BINDING PROTEIN / EF HAND / NEURONAL CALCIUM SENSING (NCS) FAMILY PROTEIN / INHIBITS RHODOPSIN KINASE / RHODOPSIN KINASE / RETINA
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / regulation of calcium ion transport / phototransduction / photoreceptor outer segment / regulation of signal transduction / photoreceptor inner segment / visual perception / perikaryon / calcium ion binding / membrane / cytosol
Similarity search - Function
Recoverin family / EF hand domain / 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 domain / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsPrem Kumar, R. / Ranaghan, M.J. / Oprian, D.D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A Highly Conserved Cysteine of Neuronal Calcium-sensing Proteins Controls Cooperative Binding of Ca2+ to Recoverin.
Authors: Ranaghan, M.J. / Kumar, R.P. / Chakrabarti, K.S. / Buosi, V. / Kern, D. / Oprian, D.D.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Sep 20, 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_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: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2872
Polymers23,2471
Non-polymers401
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.220, 84.220, 59.600
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 / p26


Mass: 23247.152 Da / Num. of mol.: 1 / Mutation: C39D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RCV1, RCVRN, Recoverin / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS (NEB) / 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


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→32 Å / Num. obs: 36942 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OMR

1omr


Resolution: 1.45→29.8 Å / Occupancy max: 1 / Occupancy min: 0.55 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1846 5 %
Rwork0.204 --
obs0.205 36940 99.9 %
all-25160 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.4 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 1 142 1715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061679
X-RAY DIFFRACTIONf_angle_d1.1082276
X-RAY DIFFRACTIONf_dihedral_angle_d14.311660
X-RAY DIFFRACTIONf_chiral_restr0.081242
X-RAY DIFFRACTIONf_plane_restr0.005298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48920.26291210.25562705X-RAY DIFFRACTION100
1.4892-1.5330.25461380.24082662X-RAY DIFFRACTION100
1.533-1.58250.2561410.22642713X-RAY DIFFRACTION100
1.5825-1.63910.25721430.22372682X-RAY DIFFRACTION100
1.6391-1.70470.26851570.22362685X-RAY DIFFRACTION100
1.7047-1.78230.28661280.20962688X-RAY DIFFRACTION100
1.7823-1.87620.2231580.2042670X-RAY DIFFRACTION100
1.8762-1.99370.19151560.19352684X-RAY DIFFRACTION100
1.9937-2.14760.20521530.18652717X-RAY DIFFRACTION100
2.1476-2.36370.20271390.19052661X-RAY DIFFRACTION100
2.3637-2.70550.22211250.19462741X-RAY DIFFRACTION100
2.7055-3.40790.21281510.19922702X-RAY DIFFRACTION100
3.4079-29.80630.22691360.21342784X-RAY DIFFRACTION100

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