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- PDB-5f6t: Structure of calexcitin-Gd3+ complex. -

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Basic information

Entry
Database: PDB / ID: 5f6t
TitleStructure of calexcitin-Gd3+ complex.
ComponentsCalexcitin
Keywordscalcium-binding protein / EF-hand Neuronal calcium signalling
Function / homology
Function and homology information


EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GADOLINIUM ATOM / Calexcitin
Similarity search - Component
Biological speciesDoryteuthis pealeii (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsChataigner, L. / Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site.
Authors: Chataigner, L. / Guo, J. / Erskine, P.T. / Coker, A.R. / Wood, S.P. / Gombos, Z. / Cooper, J.B.
History
DepositionDec 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references / Structure summary
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Jul 20, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calexcitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5384
Polymers22,3011
Non-polymers2373
Water54030
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.020, 77.020, 29.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Calexcitin


Mass: 22301.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Doryteuthis pealeii (longfin inshore squid)
Gene: cex / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76764
#2: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 38 % / Description: Plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M TRIS pH 8.5, 30 % PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.2→29.3 Å / Num. all: 9020 / Num. obs: 9020 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 66.2 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 6 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ccm

2ccm


Resolution: 2.201→27.353 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3044 870 5.13 %
Rwork0.215 --
obs0.2193 9020 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.5 Å2
Refinement stepCycle: LAST / Resolution: 2.201→27.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 3 30 1555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091596
X-RAY DIFFRACTIONf_angle_d1.0582131
X-RAY DIFFRACTIONf_dihedral_angle_d16.69577
X-RAY DIFFRACTIONf_chiral_restr0.04219
X-RAY DIFFRACTIONf_plane_restr0.004274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.33840.46751280.39622677X-RAY DIFFRACTION99
2.3384-2.51880.42181550.38452651X-RAY DIFFRACTION99
2.5188-2.77210.36751650.31972676X-RAY DIFFRACTION100
2.7721-3.17270.37011600.25792704X-RAY DIFFRACTION100
3.1727-3.99520.27651340.17962686X-RAY DIFFRACTION100
3.9952-27.35480.22451280.1412706X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6202-2.2682-1.09632.53020.85594.7411-0.6261-0.0716-1.0973-0.01991.30680.0297-0.05960.26890.35730.5043-0.10990.17570.929-0.56720.2958-9.03916.77619.1926
20.8671-0.0591.77532.23340.33493.64870.3396-0.65380.7073-0.007-0.08110.3011-0.3804-0.7045-0.27520.412-0.02830.28010.6531-0.25390.7467-28.102324.89427.4471
33.9868-0.33340.98174.9957-0.77034.80770.5883-0.1194-0.6322-0.0924-0.04680.69280.36950.1138-0.40860.3368-0.06610.07690.3864-0.17560.5254-22.384112.52953.1352
45.7007-0.5428-0.10241.8938-2.11316.4851-0.0036-0.3568-0.44280.11640.81580.51260.45580.9671-0.60430.3959-0.03360.14470.5086-0.19920.7343-17.819218.3235-4.9187
52.9774-0.89460.63911.97670.04513.15190.3528-0.10560.5384-0.05210.4058-0.3716-0.70710.7871-0.59260.5351-0.1760.31570.725-0.40180.9167-9.832329.9948-1.1894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 189 )

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