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- PDB-4nqi: Structure of the N-terminal I-BAR domain (1-259) of D.Discoideum IBARa -

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Basic information

Entry
Database: PDB / ID: 4nqi
TitleStructure of the N-terminal I-BAR domain (1-259) of D.Discoideum IBARa
ComponentsSH3 domain-containing protein
KeywordsSIGNALING PROTEIN / I-BAR DOMAIN / MEMBRANE REMODELLING / CYTOKINESIS / ENDOCYTOSIS / LIPID BINDING
Function / homology
Function and homology information


contractile vacuolar membrane / pore formation during contractile vacuole discharge / sorocarp stalk development / membrane invagination / intracellular water homeostasis / plasma membrane organization / vesicle organization / filopodium tip / cellular hypotonic response / clathrin-dependent endocytosis ...contractile vacuolar membrane / pore formation during contractile vacuole discharge / sorocarp stalk development / membrane invagination / intracellular water homeostasis / plasma membrane organization / vesicle organization / filopodium tip / cellular hypotonic response / clathrin-dependent endocytosis / mitotic cytokinesis / phagocytic vesicle / phagocytosis / actin filament polymerization / cytoskeletal protein binding / phosphatidylinositol binding / microtubule binding / vesicle / cytoskeleton / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / SH3 domain / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / SH3 domain-containing protein
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsWitte, G. / Faix, J. / Runge-Wollmann, P.
CitationJournal: J.Cell.Sci. / Year: 2014
Title: The inverse BAR domain protein IBARa drives membrane remodeling to control osmoregulation, phagocytosis and cytokinesis.
Authors: Linkner, J. / Witte, G. / Zhao, H. / Junemann, A. / Nordholz, B. / Runge-Wollmann, P. / Lappalainen, P. / Faix, J.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3 domain-containing protein
B: SH3 domain-containing protein
C: SH3 domain-containing protein
D: SH3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,4069
Polymers120,9704
Non-polymers4365
Water4,972276
1
A: SH3 domain-containing protein
B: SH3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6974
Polymers60,4852
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-55 kcal/mol
Surface area22750 Å2
MethodPISA
2
C: SH3 domain-containing protein
D: SH3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7095
Polymers60,4852
Non-polymers2243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-67 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.100, 60.210, 147.620
Angle α, β, γ (deg.)90.00, 100.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SH3 domain-containing protein


Mass: 30242.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0274805 / Production host: Escherichia coli (E. coli) / References: UniProt: C7FZZ0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE AMPLIFIED THE GENE FROM GENOMIC DNA OF D.DISCOIDEUM AX2 LABORATORY STRAIN AND THE ...AUTHORS HAVE AMPLIFIED THE GENE FROM GENOMIC DNA OF D.DISCOIDEUM AX2 LABORATORY STRAIN AND THE SEQUENCE REPORTED IS PRESENT IN THE STRAINS USED IN THE PRESENT WORK. THE GENOME DATA IN THE DATABASES REFER TO LAB STRAIN AX4. (E.G. DICTYBASE)

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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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 3350, 0.25M ammonium acetate, 15% v/v glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 100735 / Num. obs: 99218 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Net I/σ(I): 10.21
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 2.48 % / Mean I/σ(I) obs: 1.88 / Num. unique all: 7425 / % possible all: 85.3

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.21→48.401 Å / SU ML: 0.26 / σ(F): 0.88 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 2562 4.99 %random
Rwork0.1944 ---
obs0.1962 99167 98.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→48.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7249 0 29 276 7554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047351
X-RAY DIFFRACTIONf_angle_d0.7669860
X-RAY DIFFRACTIONf_dihedral_angle_d15.8932909
X-RAY DIFFRACTIONf_chiral_restr0.0491142
X-RAY DIFFRACTIONf_plane_restr0.0031291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2065-2.23160.38141120.31562183X-RAY DIFFRACTION68
2.2316-2.25780.33071620.283087X-RAY DIFFRACTION99
2.2578-2.28540.33581670.27363246X-RAY DIFFRACTION100
2.2854-2.31430.28321630.26763183X-RAY DIFFRACTION100
2.3143-2.34480.30691700.25593212X-RAY DIFFRACTION100
2.3448-2.37690.31441660.253180X-RAY DIFFRACTION100
2.3769-2.41080.321700.24733206X-RAY DIFFRACTION100
2.4108-2.44680.30781580.24013101X-RAY DIFFRACTION100
2.4468-2.4850.241710.22543218X-RAY DIFFRACTION100
2.485-2.52580.2541660.22783146X-RAY DIFFRACTION100
2.5258-2.56930.32851730.21993241X-RAY DIFFRACTION100
2.5693-2.61610.30211680.22343154X-RAY DIFFRACTION100
2.6161-2.66640.23461670.21013157X-RAY DIFFRACTION100
2.6664-2.72080.25141680.19423249X-RAY DIFFRACTION100
2.7208-2.77990.24661620.18893105X-RAY DIFFRACTION100
2.7799-2.84460.22451730.19643224X-RAY DIFFRACTION100
2.8446-2.91570.26421660.19893185X-RAY DIFFRACTION100
2.9157-2.99460.2351670.19533170X-RAY DIFFRACTION100
2.9946-3.08270.25581680.19393187X-RAY DIFFRACTION100
3.0827-3.18210.22261670.19743162X-RAY DIFFRACTION100
3.1821-3.29590.24491680.19343200X-RAY DIFFRACTION100
3.2959-3.42780.21441680.19033171X-RAY DIFFRACTION100
3.4278-3.58370.22941650.1833176X-RAY DIFFRACTION100
3.5837-3.77260.23931630.1643168X-RAY DIFFRACTION99
3.7726-4.00890.1561710.15963208X-RAY DIFFRACTION99
4.0089-4.31820.19791680.15123138X-RAY DIFFRACTION99
4.3182-4.75240.17821620.16073126X-RAY DIFFRACTION99
4.7524-5.43930.19951690.18273166X-RAY DIFFRACTION99
5.4393-6.84990.27011660.23373153X-RAY DIFFRACTION99
6.8499-48.41270.17051680.17523113X-RAY DIFFRACTION97

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