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- PDB-3ok8: I-BAR OF PinkBAR -

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Basic information

Entry
Database: PDB / ID: 3ok8
TitleI-BAR OF PinkBAR
ComponentsBrain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2
KeywordsPROTEIN BINDING / I-BAR
Function / homology
Function and homology information


: / clathrin complex / plasma membrane organization / actin crosslink formation / cell-cell contact zone / membrane organization / vesicle membrane / positive regulation of actin filament polymerization / actin filament bundle assembly / cytoplasmic vesicle membrane ...: / clathrin complex / plasma membrane organization / actin crosslink formation / cell-cell contact zone / membrane organization / vesicle membrane / positive regulation of actin filament polymerization / actin filament bundle assembly / cytoplasmic vesicle membrane / phospholipid binding / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
I-BAR domain containing protein Pinkbar / Pinkbar, SH3 / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ...I-BAR domain containing protein Pinkbar / Pinkbar, SH3 / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBoczkowska, M. / Rebowski, G. / Saarikangas, J. / Lappalainen, P. / Dominguez, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Pinkbar is an epithelial-specific BAR domain protein that generates planar membrane structures.
Authors: Pykalainen, A. / Boczkowska, M. / Zhao, H. / Saarikangas, J. / Rebowski, G. / Jansen, M. / Hakanen, J. / Koskela, E.V. / Peranen, J. / Vihinen, H. / Jokitalo, E. / Salminen, M. / Ikonen, E. ...Authors: Pykalainen, A. / Boczkowska, M. / Zhao, H. / Saarikangas, J. / Rebowski, G. / Jansen, M. / Hakanen, J. / Koskela, E.V. / Peranen, J. / Vihinen, H. / Jokitalo, E. / Salminen, M. / Ikonen, E. / Dominguez, R. / Lappalainen, P.
History
DepositionAug 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2011Group: Database references
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2
B: Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7103
Polymers52,6182
Non-polymers921
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-55 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.920, 39.913, 120.702
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Brain-specific angiogenesis inhibitor 1-associated protein 2-like protein 2 / BAI1-associated protein 2-like protein 2


Mass: 26309.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Baiap2l2, PinkBAR / Plasmid: PTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q80Y61
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growpH: 7.5
Details: 20MM HEPES, 250MM NACL, 5% GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2009 / Details: MIRRORS
RadiationMonochromator: CRYOGENICALLY-COOLED SI(111) DOUBLE-CRYSTAL SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 22999 / Num. obs: 21987 / % possible obs: 95.6 % / Redundancy: 11.8 % / Net I/σ(I): 24.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3 / % possible all: 80

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Processing

Software
NameVersionClassification
CCP4MOLREPmodel building
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→37.05 Å / SU ML: 0.38 / σ(F): 1.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1094 5 %random
Rwork0.221 ---
all0.225 22999 --
obs0.225 21871 95.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.63 Å2 / ksol: 0.35 e/Å3
Refinement stepCycle: LAST / Resolution: 2.25→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 6 283 3917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073867
X-RAY DIFFRACTIONf_angle_d0.9575219
X-RAY DIFFRACTIONf_dihedral_angle_d20.4881527
X-RAY DIFFRACTIONf_chiral_restr0.072551
X-RAY DIFFRACTIONf_plane_restr0.003689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.35240.36131140.34762157X-RAY DIFFRACTION79
2.3524-2.47640.33931250.25712372X-RAY DIFFRACTION89
2.4764-2.63150.29941350.24962595X-RAY DIFFRACTION96
2.6315-2.83460.32031430.24062709X-RAY DIFFRACTION99
2.8346-3.11980.28031420.22462690X-RAY DIFFRACTION100
3.1198-3.57090.30711440.21122718X-RAY DIFFRACTION99
3.5709-4.49770.23681420.1792719X-RAY DIFFRACTION99
4.4977-37.05220.25441490.21022817X-RAY DIFFRACTION100

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