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- PDB-2efl: Crystal structure of the EFC domain of formin-binding protein 17 -

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Basic information

Entry
Database: PDB / ID: 2efl
TitleCrystal structure of the EFC domain of formin-binding protein 17
ComponentsFormin-binding protein 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / EFC domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


membrane organization / clathrin-coated pit / endocytosis / Clathrin-mediated endocytosis / cell cortex / cytoplasmic vesicle / lysosome / cytoskeleton / lipid binding / identical protein binding / cytosol
Similarity search - Function
Formin-binding protein 1 / Formin-binding protein 1, F-BAR domain / Arfaptin homology (AH) domain/BAR domain / REM-1 domain profile. / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily ...Formin-binding protein 1 / Formin-binding protein 1, F-BAR domain / Arfaptin homology (AH) domain/BAR domain / REM-1 domain profile. / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / 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
Formin-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsShimada, A. / Niwa, H. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Curved EFC/F-BAR-Domain Dimers Are Joined End to End into a Filament for Membrane Invagination in Endocytosis
Authors: Shimada, A. / Niwa, H. / Tsujita, K. / Suetsugu, S. / Nitta, K. / Hanawa-Suetsugu, K. / Akasaka, R. / Nishino, Y. / Toyama, M. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Yamamoto, M. / Terada, ...Authors: Shimada, A. / Niwa, H. / Tsujita, K. / Suetsugu, S. / Nitta, K. / Hanawa-Suetsugu, K. / Akasaka, R. / Nishino, Y. / Toyama, M. / Chen, L. / Liu, Z.-J. / Wang, B.-C. / Yamamoto, M. / Terada, T. / Miyazawa, A. / Tanaka, A. / Sugano, S. / Shirouzu, M. / Nagayama, K. / Takenawa, T. / Yokoyama, S.
History
DepositionFeb 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formin-binding protein 1


Theoretical massNumber of molelcules
Total (without water)36,4621
Polymers36,4621
Non-polymers00
Water2,162120
1
A: Formin-binding protein 1

A: Formin-binding protein 1


Theoretical massNumber of molelcules
Total (without water)72,9252
Polymers72,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9330 Å2
ΔGint-74 kcal/mol
Surface area29660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)200.985, 41.397, 56.467
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x,y,-z+1

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Components

#1: Protein Formin-binding protein 1 / Formin-binding protein 17 / hFBP17


Mass: 36462.418 Da / Num. of mol.: 1 / Fragment: EFC DOMAIN, residues 1-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / References: UniProt: Q96RU3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% Isopropanol, 20mM magnesium chloride, 50mM MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 14, 2005
RadiationMonochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 12632 / Num. obs: 12632 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.6 / Num. unique all: 858 / % possible all: 62.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EFK

2efk


Resolution: 2.61→42.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2049786.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1247 10.3 %RANDOM
Rwork0.212 ---
all0.218 14148 --
obs0.212 12110 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2993 Å2 / ksol: 0.334458 e/Å3
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--19.81 Å20 Å27.26 Å2
2--33.05 Å20 Å2
3----13.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.61→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 0 120 2466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.91.5
X-RAY DIFFRACTIONc_mcangle_it6.232
X-RAY DIFFRACTIONc_scbond_it8.252
X-RAY DIFFRACTIONc_scangle_it12.712.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 109 8.9 %
Rwork0.268 1115 -
obs--52.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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