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- PDB-3ter: Crystal structure of SOAR domain with Inhibition helix from C. elegans -

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Basic information

Entry
Database: PDB / ID: 3ter
TitleCrystal structure of SOAR domain with Inhibition helix from C. elegans
ComponentsMammalian stromal interaction molecule-1
KeywordsMETAL BINDING PROTEIN / dimer
Function / homology
Function and homology information


Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ion homeostasis / ovulation / positive regulation of engulfment of apoptotic cell / reproductive process / store-operated calcium entry / intracellular organelle / positive regulation of smooth muscle contraction / calcium channel regulator activity / calcium channel activity ...Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ion homeostasis / ovulation / positive regulation of engulfment of apoptotic cell / reproductive process / store-operated calcium entry / intracellular organelle / positive regulation of smooth muscle contraction / calcium channel regulator activity / calcium channel activity / intracellular calcium ion homeostasis / neuronal cell body / calcium ion binding / dendrite / endoplasmic reticulum / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #3550 / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Stromal interaction molecule 1 / :
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.551 Å
AuthorsYang, X. / Jin, H. / Cai, X. / Shen, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and mechanistic insights into the activation of Stromal interaction molecule 1 (STIM1).
Authors: Yang, X. / Jin, H. / Cai, X. / Li, S. / Shen, Y.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 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: Mammalian stromal interaction molecule-1
B: Mammalian stromal interaction molecule-1


Theoretical massNumber of molelcules
Total (without water)31,2342
Polymers31,2342
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-16 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.988, 76.988, 64.797
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Mammalian stromal interaction molecule-1


Mass: 15616.843 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 256-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: stim-1, Y55B1BM.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9N379, UniProt: G5EF60*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 15% Tacsimate pH 7.0, 2% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9791
SYNCHROTRONSSRF BL17U20.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 23, 2011
ADSC QUANTUM 315r2CCDJun 9, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 12045 / Num. obs: 10722 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.047 / Rsym value: 0.056 / Net I/σ(I): 19
Reflection shellResolution: 2.55→2.64 Å / % possible all: 91.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.551→29.644 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 1156 10.17 %RASOM
Rwork0.1914 ---
all0.2017 11317 --
obs0.1985 10161 81.3 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 81.258 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7951 Å2-0 Å20 Å2
2---2.7951 Å2-0 Å2
3---5.5903 Å2
Refinement stepCycle: LAST / Resolution: 2.551→29.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 0 32 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081914
X-RAY DIFFRACTIONf_angle_d1.1522562
X-RAY DIFFRACTIONf_dihedral_angle_d20.267746
X-RAY DIFFRACTIONf_chiral_restr0.076293
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5508-2.66680.34161290.28541176X-RAY DIFFRACTION75
2.6668-2.80730.33971380.25091252X-RAY DIFFRACTION80
2.8073-2.9830.29511560.22681299X-RAY DIFFRACTION83
2.983-3.21310.30281610.20721358X-RAY DIFFRACTION86
3.2131-3.5360.25791500.17241353X-RAY DIFFRACTION87
3.536-4.04660.24521510.16321357X-RAY DIFFRACTION85
4.0466-5.0940.20331390.1431293X-RAY DIFFRACTION83
5.094-29.64560.28761320.241127X-RAY DIFFRACTION72
Refinement TLS params.Method: refined / Origin x: -19.0184 Å / Origin y: -11.4072 Å / Origin z: 9.0294 Å
111213212223313233
T0.3396 Å20.0099 Å2-0.0026 Å2-0.3009 Å2-0.0087 Å2--0.4479 Å2
L2.0548 °2-0.0536 °2-0.1311 °2-1.5149 °2-0.1913 °2--0.1206 °2
S-0.1851 Å °-0.1543 Å °0.1842 Å °-0.2173 Å °0.024 Å °0.0459 Å °0.0473 Å °0.0235 Å °0.1566 Å °
Refinement TLS groupSelection details: all

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