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- PDB-1tjm: Crystallographic Identification of Sr2+ Coordination Site in Syna... -

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Basic information

Entry
Database: PDB / ID: 1tjm
TitleCrystallographic Identification of Sr2+ Coordination Site in Synaptotagmin I C2B Domain
ComponentsSynaptotagmin I
KeywordsENDOCYTOSIS/EXOCYTOSIS / Synaptotagmin I / C2B domain / Strontium binding / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane ...regulation of vesicle fusion / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / chromaffin granule membrane / calcium ion-regulated exocytosis of neurotransmitter / Glutamate Neurotransmitter Release Cycle / calcium ion sensor activity / Norepinephrine Neurotransmitter Release Cycle / regulation of calcium ion-dependent exocytosis / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / exocytic vesicle / positive regulation of calcium ion-dependent exocytosis / vesicle organization / protein heterooligomerization / positive regulation of dendrite extension / vesicle docking / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of dopamine secretion / calcium-ion regulated exocytosis / vesicle fusion / dense core granule / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / neurotransmitter secretion / syntaxin binding / presynaptic active zone / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / regulation of dopamine secretion / excitatory synapse / synaptic vesicle exocytosis / detection of calcium ion / positive regulation of synaptic transmission / postsynaptic cytosol / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / secretory granule / hippocampal mossy fiber to CA3 synapse / SNARE binding / molecular condensate scaffold activity / response to calcium ion / phospholipid binding / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / presynaptic membrane / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / calcium ion binding / lipid binding / glutamatergic synapse / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
STRONTIUM ION / Synaptotagmin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsCheng, Y. / Sequeira, S.M. / Malinina, L. / Tereshko, V. / Sollner, T.H. / Patel, D.J.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain
Authors: Cheng, Y. / Sequeira, S.M. / Malinina, L. / Tereshko, V. / Sollner, T.H. / Patel, D.J.
History
DepositionJun 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Synaptotagmin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0023
Polymers17,8231
Non-polymers1802
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.644, 54.644, 103.317
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Synaptotagmin I / SytI / p65


Mass: 17822.727 Da / Num. of mol.: 1 / Fragment: C2B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: SYT1, SYT / Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21707
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.18→20 Å / Num. obs: 56844 / % possible obs: 95.5 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 31.1
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.4 / % possible all: 56.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1K5W

1k5w


Resolution: 1.18→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.37 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17373 2861 5 %RANDOM
Rwork0.15818 ---
obs0.15897 53935 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.18→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 7 202 1437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221282
X-RAY DIFFRACTIONr_bond_other_d0.0020.021196
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9681729
X-RAY DIFFRACTIONr_angle_other_deg0.91232810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021377
X-RAY DIFFRACTIONr_gen_planes_other0.020.02234
X-RAY DIFFRACTIONr_nbd_refined0.2440.2260
X-RAY DIFFRACTIONr_nbd_other0.2510.21395
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2817
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7021.5777
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.62721267
X-RAY DIFFRACTIONr_scbond_it3.2013505
X-RAY DIFFRACTIONr_scangle_it5.0414.5462
X-RAY DIFFRACTIONr_rigid_bond_restr1.72121282
X-RAY DIFFRACTIONr_sphericity_free5.0622203
X-RAY DIFFRACTIONr_sphericity_bonded3.95521260
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.229 118
Rwork0.247 2536

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