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- PDB-6ixe: Crystal structure of SeMet apo SH3BP5 (I41) -

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Basic information

Entry
Database: PDB / ID: 6ixe
TitleCrystal structure of SeMet apo SH3BP5 (I41)
ComponentsSH3 domain-binding protein 5
KeywordsSIGNALING PROTEIN / Rab11 / GEF / SH3BP5
Function / homology
Function and homology information


protein kinase inhibitor activity / guanyl-nucleotide exchange factor activity / cytoplasmic vesicle membrane / SH3 domain binding / nuclear body / intracellular signal transduction / signal transduction / mitochondrion / nucleoplasm / cytoplasm
Similarity search - Function
SH3-binding 5 / SH3 domain-binding protein 5 (SH3BP5)
Similarity search - Domain/homology
SUCCINIC ACID / SH3 domain-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.35 Å
AuthorsGoto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science17K15072 Japan
CitationJournal: Life Sci Alliance / Year: 2019
Title: Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5.
Authors: Goto-Ito, S. / Morooka, N. / Yamagata, A. / Sato, Y. / Sato, K. / Fukai, S.
History
DepositionDec 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 domain-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8092
Polymers26,6901
Non-polymers1181
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.250, 79.250, 108.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein SH3 domain-binding protein 5 / SH3BP-5 / SH3 domain-binding protein that preferentially associates with BTK


Mass: 26690.434 Da / Num. of mol.: 1 / Mutation: M167A,R260A,R261A,R262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SH3BP5, SAB / Production host: Escherichia coli (E. coli) / References: UniProt: O60239
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4

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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: 3.18 Å3/Da / Density % sol: 61.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M succinic acid (pH 7.0), 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 4777 / % possible obs: 96.9 % / Redundancy: 8.2 % / Rsym value: 0.158 / Net I/σ(I): 30
Reflection shellResolution: 3.35→3.41 Å / Rsym value: 0.357

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.35→38.899 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 42.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3138 239 5.1 %
Rwork0.2691 --
obs0.2714 4689 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→38.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 8 0 1745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031762
X-RAY DIFFRACTIONf_angle_d0.6582357
X-RAY DIFFRACTIONf_dihedral_angle_d11.417702
X-RAY DIFFRACTIONf_chiral_restr0.019262
X-RAY DIFFRACTIONf_plane_restr0.002306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3505-4.22040.38591170.35482162X-RAY DIFFRACTION95
4.2204-38.90110.28531220.23982288X-RAY DIFFRACTION99

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