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- PDB-4mlw: Crystal structure of non-myristoylated recoverin at 1.45 A resolu... -

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Basic information

Entry
Database: PDB / ID: 4mlw
TitleCrystal structure of non-myristoylated recoverin at 1.45 A resolution with calcium 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
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 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_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_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

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Assembly

Deposited unit
A: Recoverin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2752
Polymers23,2351
Non-polymers401
Water3,081171
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_535-x,-y-2,z1
crystal symmetry operation3_445-y-1,x-1,z1
crystal symmetry operation4_645y+1,-x-1,z1
Buried area8960 Å2
ΔGint-97 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.720, 84.720, 58.850
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: 23235.209 Da / Num. of mol.: 1
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.: 171 / 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: 45.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M Ammonium citrate, 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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2012 / 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→31.86 Å / Num. all: 36801 / Num. obs: 36801 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1omr


Resolution: 1.45→31.857 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.15 / σ(F): 1.33 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1839 5 %
Rwork0.1896 --
obs0.1907 36790 99.51 %
all-36801 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.2922 Å2
Refinement stepCycle: LAST / Resolution: 1.45→31.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 1 171 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061714
X-RAY DIFFRACTIONf_angle_d1.162330
X-RAY DIFFRACTIONf_dihedral_angle_d15.813683
X-RAY DIFFRACTIONf_chiral_restr0.081247
X-RAY DIFFRACTIONf_plane_restr0.005308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48920.2781670.25712663X-RAY DIFFRACTION100
1.4892-1.5330.25081410.23842659X-RAY DIFFRACTION100
1.533-1.58250.21981320.22222712X-RAY DIFFRACTION100
1.5825-1.63910.22581310.212706X-RAY DIFFRACTION100
1.6391-1.70470.24121370.20292690X-RAY DIFFRACTION100
1.7047-1.78230.22741370.20292694X-RAY DIFFRACTION100
1.7823-1.87620.21231430.19192702X-RAY DIFFRACTION100
1.8762-1.99380.20861450.18452656X-RAY DIFFRACTION100
1.9938-2.14770.18911560.18022696X-RAY DIFFRACTION100
2.1477-2.36370.19881400.18262706X-RAY DIFFRACTION100
2.3637-2.70560.21181370.18522697X-RAY DIFFRACTION100
2.7056-3.40820.1911340.18522720X-RAY DIFFRACTION99
3.4082-31.86440.22571390.18572650X-RAY DIFFRACTION95

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