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- PDB-3syv: Crystal structure of mPACSIN 3 F-BAR domain mutant -

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Basic information

Entry
Database: PDB / ID: 3syv
TitleCrystal structure of mPACSIN 3 F-BAR domain mutant
ComponentsProtein kinase C and casein kinase II substrate protein 3
KeywordsENDOCYTOSIS / Alpha helix / Membrane modeling
Function / homology
Function and homology information


plasma membrane tubulation / Clathrin-mediated endocytosis / negative regulation of endocytosis / positive regulation of membrane protein ectodomain proteolysis / negative regulation of calcium ion transport / regulation of endocytosis / calcium channel inhibitor activity / cytoskeleton organization / cytoskeletal protein binding / phospholipid binding ...plasma membrane tubulation / Clathrin-mediated endocytosis / negative regulation of endocytosis / positive regulation of membrane protein ectodomain proteolysis / negative regulation of calcium ion transport / regulation of endocytosis / calcium channel inhibitor activity / cytoskeleton organization / cytoskeletal protein binding / phospholipid binding / endocytosis / endosome / lipid binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arfaptin homology (AH) domain/BAR domain / 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 ...Arfaptin homology (AH) domain/BAR domain / 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
Protein kinase C and casein kinase II substrate protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBai, X.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Rigidity of wedge loop in PACSIN 3 protein is a key factor in dictating diameters of tubules
Authors: Bai, X. / Meng, G. / Luo, M. / Zheng, X.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein kinase C and casein kinase II substrate protein 3
B: Protein kinase C and casein kinase II substrate protein 3
C: Protein kinase C and casein kinase II substrate protein 3
D: Protein kinase C and casein kinase II substrate protein 3
E: Protein kinase C and casein kinase II substrate protein 3
F: Protein kinase C and casein kinase II substrate protein 3
G: Protein kinase C and casein kinase II substrate protein 3
H: Protein kinase C and casein kinase II substrate protein 3


Theoretical massNumber of molelcules
Total (without water)323,4418
Polymers323,4418
Non-polymers00
Water1,964109
1
A: Protein kinase C and casein kinase II substrate protein 3
B: Protein kinase C and casein kinase II substrate protein 3


Theoretical massNumber of molelcules
Total (without water)80,8602
Polymers80,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-46 kcal/mol
Surface area27870 Å2
MethodPISA
2
C: Protein kinase C and casein kinase II substrate protein 3
D: Protein kinase C and casein kinase II substrate protein 3


Theoretical massNumber of molelcules
Total (without water)80,8602
Polymers80,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-45 kcal/mol
Surface area27910 Å2
MethodPISA
3
E: Protein kinase C and casein kinase II substrate protein 3
F: Protein kinase C and casein kinase II substrate protein 3


Theoretical massNumber of molelcules
Total (without water)80,8602
Polymers80,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-44 kcal/mol
Surface area27250 Å2
MethodPISA
4
G: Protein kinase C and casein kinase II substrate protein 3
H: Protein kinase C and casein kinase II substrate protein 3


Theoretical massNumber of molelcules
Total (without water)80,8602
Polymers80,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-37 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.570, 108.901, 222.319
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein kinase C and casein kinase II substrate protein 3


Mass: 40430.082 Da / Num. of mol.: 8 / Fragment: UNP residues 1-341 / Mutation: P121Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pacsin3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99JB8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 4.51 Å3/Da / Density % sol: 72.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 1.0M Lithium sulfate monohydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.9 Å / Num. obs: 99512 / % possible obs: 98.68 %
Reflection shellResolution: 3.1→3.18 Å / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.9 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.881 / SU B: 17.957 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33683 5196 5 %RANDOM
Rwork0.28063 ---
obs0.28345 98202 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16361 0 0 109 16470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02116732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.9222482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85452007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70122.663920
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.909152867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.20315197
X-RAY DIFFRACTIONr_chiral_restr0.1350.22239
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213061
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_it4.4951.510016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.304215710
X-RAY DIFFRACTIONr_scbond_it3.00236716
X-RAY DIFFRACTIONr_scangle_it5.2784.56772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 357 -
Rwork0.357 7200 -
obs--98.02 %

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