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- PDB-6o2v: Crystal structure of the SARAF luminal domain Cys-lock mutant monomer -

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Basic information

Entry
Database: PDB / ID: 6o2v
TitleCrystal structure of the SARAF luminal domain Cys-lock mutant monomer
ComponentsStore-operated calcium entry-associated regulatory factor
KeywordsSIGNALING PROTEIN / SOCE / Store Operated Calcium Entry / SARAF / ER / Endoplasmic reticulum / Calcium signaling / Domain swap
Function / homologyStore-operated calcium entry-associated regulatory factor / SOCE-associated regulatory factor of calcium homoeostasis / endoplasmic reticulum-plasma membrane contact site / regulation of store-operated calcium entry / calcium ion transport / endoplasmic reticulum membrane / endoplasmic reticulum / FORMIC ACID / Store-operated calcium entry-associated regulatory factor
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKimberlin, C.R. / Minor, D.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL080050 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01-DC007664 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32HL007731 United States
American Heart Association14POST18740062 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: SARAF Luminal Domain Structure Reveals a Novel Domain-Swapped beta-Sandwich Fold Important for SOCE Modulation.
Authors: Kimberlin, C.R. / Meshcheriakova, A. / Palty, R. / Raveh, A. / Karbat, I. / Reuveny, E. / Minor Jr., D.L.
History
DepositionFeb 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Store-operated calcium entry-associated regulatory factor
B: Store-operated calcium entry-associated regulatory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1854
Polymers31,0472
Non-polymers1382
Water5,513306
1
A: Store-operated calcium entry-associated regulatory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5692
Polymers15,5231
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Store-operated calcium entry-associated regulatory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6152
Polymers15,5231
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.689, 60.953, 63.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Store-operated calcium entry-associated regulatory factor / SOCE-associated regulatory factor / HBV X-transactivated gene 3 protein / HBV XAg-transactivated ...SOCE-associated regulatory factor / HBV X-transactivated gene 3 protein / HBV XAg-transactivated protein 3 / Protein FOAP-7 / Transmembrane protein 66


Mass: 15523.334 Da / Num. of mol.: 2 / Mutation: K98C, A156C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: SARAF, TMEM66, XTP3, HSPC035, NPD003, PSEC0019, UNQ1967/PRO4499
Production host: Escherichia coli (E. coli) / References: UniProt: Q96BY9
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 1.86 Å3/Da / Density % sol: 33.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M sodium acetate, pH 4.2-4.6 and 1.2-1.6M sodium formate
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.58→63.441 Å / Num. obs: 32028 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 11.85 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Rsym value: 0.084 / Net I/av σ(I): 8.4 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.58-1.664.30.5191.542140.3050.6510.51991.5
1.66-1.776.40.4221.844210.1940.4990.42299.6
1.77-1.897.20.2872.641370.1220.3320.287100
1.89-2.047.20.1774.339030.0750.2040.177100
2.04-2.237.20.126.335850.0520.1390.12100
2.23-2.57.20.0928.232750.0390.1060.092100
2.5-2.887.10.06910.929050.030.080.069100
2.88-3.5370.04416.324830.0190.050.044100
3.53-4.996.70.0320.819510.0130.0350.03100
4.99-63.4416.40.03117.311540.0140.0360.03199.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O2U

6o2u


Resolution: 1.58→43.954 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.64
RfactorNum. reflection% reflection
Rfree0.2032 1620 5.07 %
Rwork0.1654 --
obs0.1674 31922 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.45 Å2 / Biso mean: 14.7208 Å2 / Biso min: 3.32 Å2
Refinement stepCycle: final / Resolution: 1.58→43.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 9 320 2448
Biso mean--25.77 23.28 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062249
X-RAY DIFFRACTIONf_angle_d0.8543064
X-RAY DIFFRACTIONf_chiral_restr0.051314
X-RAY DIFFRACTIONf_plane_restr0.005400
X-RAY DIFFRACTIONf_dihedral_angle_d14.125835
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.62650.24331060.21832202230888
1.6265-1.6790.26591290.2082413254296
1.679-1.7390.24471250.1962548267399
1.739-1.80860.2541280.18825322660100
1.8086-1.8910.21051360.165225092645100
1.891-1.99070.18121270.159925602687100
1.9907-2.11540.20481420.163325312673100
2.1154-2.27870.23391740.158725152689100
2.2787-2.5080.24051370.16725722709100
2.508-2.87080.20771370.166725742711100
2.8708-3.61670.16781330.146426122745100
3.6167-43.97050.16611460.158127342880100

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