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- PDB-6b26: Crystal structure of human STAC2 Tandem SH3 Domains (296-411) -

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Basic information

Entry
Database: PDB / ID: 6b26
TitleCrystal structure of human STAC2 Tandem SH3 Domains (296-411)
ComponentsSH3 and cysteine-rich domain-containing protein 2
KeywordsPROTEIN BINDING / Excitation-contraction coupling / ion channel adaptor protein
Function / homology
Function and homology information


positive regulation of voltage-gated calcium channel activity / skeletal muscle contraction / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of protein localization to plasma membrane / sarcolemma / cytoplasmic side of plasma membrane / metal ion binding / cytosol
Similarity search - Function
Stac2, SH3 domain / STAC1/2/3 / Unstructured on SH3 and cysteine-rich domain-containing protein 2 / Variant SH3 domain / Variant SH3 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...Stac2, SH3 domain / STAC1/2/3 / Unstructured on SH3 and cysteine-rich domain-containing protein 2 / Variant SH3 domain / Variant SH3 domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SH3 and cysteine-rich domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWong King Yuen, S.M. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-119608 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural insights into binding of STAC proteins to voltage-gated calcium channels.
Authors: Wong King Yuen, S.M. / Campiglio, M. / Tung, C.C. / Flucher, B.E. / Van Petegem, F.
History
DepositionSep 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
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
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: SH3 and cysteine-rich domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,4711
Polymers13,4711
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.857, 47.993, 73.587
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 SH3 and cysteine-rich domain-containing protein 2 / 24b2/STAC2 / Src homology 3 and cysteine-rich domain-containing protein 2


Mass: 13471.185 Da / Num. of mol.: 1 / Fragment: residues 296-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZMT1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 277.15 K / Method: microdialysis / pH: 7.4 / Details: 150mM KCl, 10mM HEPES, 2mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.2→32.95 Å / Num. obs: 41292 / % possible obs: 99.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.02397 / Net I/σ(I): 29.89
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.2007 / Mean I/σ(I) obs: 5.84 / % possible all: 98.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DL4

2dl4


Resolution: 1.2→32.95 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.042 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0393 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.037
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 2040 4.9 %RANDOM
Rwork0.1524 ---
obs0.1532 39292 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 50.72 Å2 / Biso mean: 14.152 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å20 Å2
2--0.28 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.2→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 240 1168
Biso mean---26.36 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021044
X-RAY DIFFRACTIONr_bond_other_d0.0020.02990
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9591430
X-RAY DIFFRACTIONr_angle_other_deg0.90232316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50323.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.271511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02229
X-RAY DIFFRACTIONr_rigid_bond_restr2.41432034
X-RAY DIFFRACTIONr_sphericity_free13.6455139
X-RAY DIFFRACTIONr_sphericity_bonded3.25952100
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 132 -
Rwork0.179 2878 -
all-3010 -
obs--98.72 %

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