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- PDB-5vei: Crystal structure of the SH3 domain of human sorbin and SH3 domai... -

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Basic information

Entry
Database: PDB / ID: 5vei
TitleCrystal structure of the SH3 domain of human sorbin and SH3 domain-containing protein 2
ComponentsSorbin and SH3 domain-containing protein 2
KeywordsPROTEIN BINDING / Structural Genomics Consortium / SGC / SH3 / Src Homology 3 domain
Function / homology
Function and homology information


cell growth involved in cardiac muscle cell development / cytoskeletal anchor activity / structural constituent of muscle / Notch signaling pathway / actin filament organization / structural constituent of cytoskeleton / Z disc / actin cytoskeleton / lamellipodium / apical plasma membrane ...cell growth involved in cardiac muscle cell development / cytoskeletal anchor activity / structural constituent of muscle / Notch signaling pathway / actin filament organization / structural constituent of cytoskeleton / Z disc / actin cytoskeleton / lamellipodium / apical plasma membrane / focal adhesion / perinuclear region of cytoplasm / RNA binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Sorbin and SH3 domain-containing protein / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Variant SH3 domain / SH3 Domains / Zinc finger C2H2-type / SH3 domain / SH3 type barrels. ...Sorbin and SH3 domain-containing protein / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Variant SH3 domain / SH3 Domains / Zinc finger C2H2-type / SH3 domain / 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
Sorbin and SH3 domain-containing protein 2 / Sorbin and SH3 domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsLiu, Y. / Tempel, W. / Huang, H. / Gu, J. / Liu, K. / Sidhu, S.S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the SH3 domain of human sorbin and SH3 domain-containing protein 2
Authors: Liu, Y. / Tempel, W. / Huang, H. / Gu, J. / Liu, K. / Sidhu, S.S. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 2, 2017ID: 4IGZ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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: Sorbin and SH3 domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)12,30628
Polymers12,3061
Non-polymers027
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.202, 27.494, 58.831
Angle α, β, γ (deg.)90.000, 101.010, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Sorbin and SH3 domain-containing protein 2 / SORBS2


Mass: 12305.836 Da / Num. of mol.: 1 / Fragment: UNP residues 215-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORBS2 / Plasmid: modified pHH0239/6His/TEV vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: H7C1R7, UniProt: O94875*PLUS
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 27 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.49 Å3/Da / Density % sol: 17.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 28% PEG2000, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.33→39.52 Å / Num. obs: 16870 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Net I/σ(I): 14.8 / Num. measured all: 60287 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.33-1.353.61.20830428460.4940.7441.4231.199.8
7.28-39.5230.0163111050.9990.0110.01946.792.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C0C

3c0c


Resolution: 1.33→12.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.054 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.056
RfactorNum. reflection% reflection
Rfree0.206 818 4.85 %
Rwork0.185 --
obs0.186 16850 99.7 %
Displacement parametersBiso max: 59.2 Å2 / Biso mean: 20.7 Å2 / Biso min: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.8751 Å20 Å2-3.6899 Å2
2--3.9683 Å20 Å2
3----7.8433 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.33→12.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 27 22 657
Biso mean--28.24 29.14 -
Num. residues----80
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d224SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes12HARMONIC2
X-RAY DIFFRACTIONt_gen_planes105HARMONIC5
X-RAY DIFFRACTIONt_it669HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion87SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact787SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d669HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg914HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.52
X-RAY DIFFRACTIONt_other_torsion13.74
LS refinement shellResolution: 1.33→1.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.226 151 4.98 %
Rwork0.223 2881 -
all-3032 -
obs--99.67 %

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