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- PDB-2ydl: Crystal structure of SH3C from CIN85 -

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Basic information

Entry
Database: PDB / ID: 2ydl
TitleCrystal structure of SH3C from CIN85
ComponentsSH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / cytoplasmic vesicle membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / InlB-mediated entry of Listeria monocytogenes into host cell / actin filament organization / GABA-ergic synapse / EGFR downregulation ...Reelin signalling pathway / positive regulation of B cell activation / endocytic vesicle / cytoskeleton organization / cytoplasmic vesicle membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / InlB-mediated entry of Listeria monocytogenes into host cell / actin filament organization / GABA-ergic synapse / EGFR downregulation / Negative regulation of MET activity / SH3 domain binding / endocytosis / cell-cell junction / cell migration / Cargo recognition for clathrin-mediated endocytosis / cell-cell signaling / regulation of cell shape / Clathrin-mediated endocytosis / Potential therapeutics for SARS / cytoskeleton / neuron projection / postsynaptic density / focal adhesion / apoptotic process / ubiquitin protein ligase binding / glutamatergic synapse / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / : / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...SH3 domain-containing kinase-binding protein 1, first SH3 domain / SH3 domain-containing kinase-binding protein 1, second SH3 domain / SH3 domain-containing kinase-binding protein 1, third SH3 domain / : / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SH3 domain-containing kinase-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBravo, J. / Cardenes, N.
CitationJournal: Plos One / Year: 2013
Title: Distinct Ubiquitin Binding Modes Exhibited by SH3 Domains: Molecular Determinants and Functional Implications.
Authors: Ortega Roldan, J.L. / Casares, S. / Ringkjobing Jensen, M. / Cardenes, N. / Bravo, J. / Blackledge, M. / Azuaga, A.I. / Van Nuland, N.A.J.
History
DepositionMar 22, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)8,0351
Polymers8,0351
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.828, 47.828, 70.235
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SH3 DOMAIN-CONTAINING KINASE-BINDING PROTEIN 1 / CD2-BINDING PROTEIN 3 / CD2BP3 / CBL-INTERACTING PROTEIN OF 85 KDA / HUMAN SRC FAMILY KINASE- ...CD2-BINDING PROTEIN 3 / CD2BP3 / CBL-INTERACTING PROTEIN OF 85 KDA / HUMAN SRC FAMILY KINASE-BINDING PROTEIN 1 / HSB-1 / CIN85


Mass: 8034.963 Da / Num. of mol.: 1 / Fragment: SH3 C, RESIDUES 270-328
Source method: isolated from a genetically manipulated source
Details: THIRD SH3 DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96B97
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 0.1M CITRATE PH 5.5, 2.0 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER FR530 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 2007 / Details: MIRROR
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→26.78 Å / Num. obs: 5991 / % possible obs: 95.4 % / Observed criterion σ(I): 6 / Redundancy: 3.13 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 8.31
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 3.13 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.2 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SEM

1sem


Resolution: 2.05→41.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.67 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25222 275 4.6 %RANDOM
Rwork0.20515 ---
obs0.2074 5715 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.791 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms547 0 0 56 603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021562
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.934763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.856565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92425.16131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.269152
X-RAY DIFFRACTIONr_chiral_restr0.1020.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021439
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9511.5332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8042537
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6043230
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3344.5226
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 15 -
Rwork0.27 417 -
obs--94.74 %

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