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- PDB-1juo: Crystal Structure of Calcium-free Human Sorcin: A Member of the P... -

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Basic information

Entry
Database: PDB / ID: 1juo
TitleCrystal Structure of Calcium-free Human Sorcin: A Member of the Penta-EF-Hand Protein Family
Componentssorcin
KeywordsMETAL TRANSPORT / calcium-binding proteins / penta-ef-hand / PEF
Function / homology
Function and homology information


regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / muscle organ development / regulation of heart contraction ...regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / muscle organ development / regulation of heart contraction / action potential / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of calcium ion transport / Ion transport by P-type ATPases / calcium channel regulator activity / intracellular sequestering of iron ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / calcium ion transport / heart development / DNA-binding transcription factor binding / protease binding / transmembrane transporter binding / protein heterodimerization activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsXie, X.
CitationJournal: Protein Sci. / Year: 2001
Title: Crystal structure of calcium-free human sorcin: a member of the penta-EF-hand protein family.
Authors: Xie, X. / Dwyer, M.D. / Swenson, L. / Parker, M.H. / Botfield, M.C.
History
DepositionAug 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sorcin
B: sorcin


Theoretical massNumber of molelcules
Total (without water)43,3912
Polymers43,3912
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-18 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.250, 118.250, 85.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein sorcin


Mass: 21695.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P30626
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium chloride, HEPES, EGTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.004 mMsorcin1drop
20.010 mMfluo-4 pentapossium salt1drop
36.4 mMurea1dropor 7.8M
40.5 M1reservoirNaCl
50.1 HEPES1reservoirpH7.0
62.5 mMEGTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 30, 1999 / Details: mirrors
RadiationMonochromator: Confocal Multilayer (Rigaku/MSC) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 167295 / Num. obs: 28472 / % possible obs: 90.7 % / Observed criterion σ(I): -1 / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1929 / % possible all: 75.3
Reflection
*PLUS
Num. measured all: 167295

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Processing

Software
NameVersionClassification
CNX2000refinement
DENZOdata reduction
SCALEPACKdata scaling
CNX2000phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→37.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 368354.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2760 9.9 %RANDOM
Rwork0.218 ---
all0.221 27925 --
obs0.221 27925 89.1 %-
Solvent computationSolvent model: flat model / Bsol: 41.8194 Å2 / ksol: 0.294676 e/Å3
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.73 Å20 Å20 Å2
2---8.73 Å20 Å2
3---17.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 0 290 2957
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 392 10.3 %
Rwork0.347 3396 -
obs--73.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNX2000 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.199
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.347

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