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- PDB-3fdw: Crystal structure of a C2 domain from human synaptotagmin-like pr... -

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Basic information

Entry
Database: PDB / ID: 3fdw
TitleCrystal structure of a C2 domain from human synaptotagmin-like protein 4
ComponentsSynaptotagmin-like protein 4
KeywordsLIPID BINDING PROTEIN / STRUCTURAL GENOMICS / PHOSPHOLIPID BINDING / Alternative splicing / Cell membrane / Cytoplasmic vesicle / Membrane / Metal-binding / Phosphoprotein / Polymorphism / Zinc / Zinc-finger / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


regulation of plasma membrane repair / neurexin family protein binding / exocytic vesicle / multivesicular body sorting pathway / platelet alpha granule membrane / lysosome localization / plasma membrane repair / insulin secretion / transport vesicle membrane / exocytosis ...regulation of plasma membrane repair / neurexin family protein binding / exocytic vesicle / multivesicular body sorting pathway / platelet alpha granule membrane / lysosome localization / plasma membrane repair / insulin secretion / transport vesicle membrane / exocytosis / positive regulation of exocytosis / negative regulation of insulin secretion / positive regulation of protein secretion / intracellular protein transport / small GTPase binding / phospholipid binding / Platelet degranulation / endosome / zinc ion binding / plasma membrane
Similarity search - Function
Synaptotagmin-like protein 4/5, C2A domain / Synaptotagmin-like protein 4 , FYVE-related domain / Synaptotagmin-like 1-5, C2B domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) ...Synaptotagmin-like protein 4/5, C2A domain / Synaptotagmin-like protein 4 , FYVE-related domain / Synaptotagmin-like 1-5, C2B domain / FYVE-type zinc finger / FYVE-type zinc finger / Rab-binding domain / Rab-binding domain profile. / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptotagmin-like protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Miller, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a C2 domain from human synaptotagmin-like protein 4
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Miller, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Synaptotagmin-like protein 4
B: Synaptotagmin-like protein 4


Theoretical massNumber of molelcules
Total (without water)34,5872
Polymers34,5872
Non-polymers00
Water2,414134
1
A: Synaptotagmin-like protein 4


Theoretical massNumber of molelcules
Total (without water)17,2941
Polymers17,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Synaptotagmin-like protein 4


Theoretical massNumber of molelcules
Total (without water)17,2941
Polymers17,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.461, 57.207, 124.083
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Synaptotagmin-like protein 4 / Exophilin-2 / Granuphilin


Mass: 17293.674 Da / Num. of mol.: 2 / Fragment: C2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYTL4 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96C24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM Tris HCl pH 8.5, 1.6M DL-malic acid pH 7, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 23, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→33.52 Å / Num. all: 18310 / Num. obs: 18310 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.9 / Num. measured all: 11509 / Num. unique all: 2720 / Rsym value: 0.23 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.896 / WRfactor Rfree: 0.986 / WRfactor Rwork: 0.976 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.747 / SU B: 6.218 / SU ML: 0.161 / SU R Cruickshank DPI: 0.266 / SU Rfree: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.266 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 945 5.2 %RANDOM
Rwork0.233 ---
obs0.236 18275 100 %-
all-18275 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 90.57 Å2 / Biso mean: 38.124 Å2 / Biso min: 17.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.01 Å2
2---0.05 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 0 134 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212124
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.952878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7065258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95523100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69115356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211614
X-RAY DIFFRACTIONr_mcbond_it1.0851.51296
X-RAY DIFFRACTIONr_mcangle_it1.95122072
X-RAY DIFFRACTIONr_scbond_it2.4573828
X-RAY DIFFRACTIONr_scangle_it3.9564.5806
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 64 -
Rwork0.259 1259 -
all-1323 -
obs-1259 100 %

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