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- PDB-5vff: Synaptotagmin 1 C2B domain, lead-bound (low occupancy) -

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Basic information

Entry
Database: PDB / ID: 5vff
TitleSynaptotagmin 1 C2B domain, lead-bound (low occupancy)
ComponentsSynaptotagmin-1
KeywordsMETAL BINDING PROTEIN / C2B DOMAIN
Function / homology
Function and homology information


GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding ...GABA synthesis, release, reuptake and degradation / Serotonin Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / Glutamate Neurotransmitter Release Cycle / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / chromaffin granule membrane / dense core granule / calcium ion sensor activity / regulation of calcium ion-dependent exocytosis / positive regulation of calcium ion-dependent exocytosis / calcium ion-regulated exocytosis of neurotransmitter / vesicle docking / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of dopamine secretion / protein heterooligomerization / Clathrin-mediated endocytosis / positive regulation of dendrite extension / neurotransmitter secretion / calcium-dependent phospholipid binding / neuron projection terminus / syntaxin binding / syntaxin-1 binding / regulation of synaptic vesicle exocytosis / low-density lipoprotein particle receptor binding / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / synaptic vesicle exocytosis / synaptic vesicle endocytosis / excitatory synapse / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / secretory granule / phospholipid binding / synaptic vesicle membrane / response to calcium ion / calcium-dependent protein binding / synaptic vesicle / presynaptic membrane / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / 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
LEAD (II) ION / Synaptotagmin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.413 Å
AuthorsTaylor, A.B. / Hart, P.J. / Igumenova, T.I.
CitationJournal: Metallomics / Year: 2018
Title: High affinity interactions of Pb2+with synaptotagmin I.
Authors: Katti, S. / Her, B. / Srivastava, A.K. / Taylor, A.B. / Lockless, S.W. / Igumenova, T.I.
History
DepositionApr 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4152
Polymers17,2081
Non-polymers2071
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint0 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.634, 41.117, 82.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 17208.006 Da / Num. of mol.: 1 / Fragment: residues 271-421 / Mutation: C277S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt1 / Plasmid: PET-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46096
#2: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium fluoride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.41→41.43 Å / Num. obs: 27034 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.1 Å2 / Rpim(I) all: 0.023 / Rsym value: 0.056 / Net I/σ(I): 22.7
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3733 / Rpim(I) all: 0.266 / Rsym value: 0.617 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UOW

1uow


Resolution: 1.413→36.483 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 17.05
RfactorNum. reflection% reflection
Rfree0.191 3755 7.44 %
Rwork0.1551 --
obs0.1577 26980 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.3 Å2
Refinement stepCycle: LAST / Resolution: 1.413→36.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 1 251 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061253
X-RAY DIFFRACTIONf_angle_d0.8871694
X-RAY DIFFRACTIONf_dihedral_angle_d21.068482
X-RAY DIFFRACTIONf_chiral_restr0.082192
X-RAY DIFFRACTIONf_plane_restr0.005214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4133-1.43120.31271290.27231474X-RAY DIFFRACTION85
1.4312-1.450.2551410.22921718X-RAY DIFFRACTION96
1.45-1.46990.19091290.20331678X-RAY DIFFRACTION96
1.4699-1.49090.25221390.18941718X-RAY DIFFRACTION98
1.4909-1.51320.20011470.17271716X-RAY DIFFRACTION97
1.5132-1.53680.2061330.16451690X-RAY DIFFRACTION98
1.5368-1.5620.19991420.15961770X-RAY DIFFRACTION98
1.562-1.58890.19071310.15511661X-RAY DIFFRACTION97
1.5889-1.61780.23461470.15281752X-RAY DIFFRACTION99
1.6178-1.64890.19981380.14731725X-RAY DIFFRACTION98
1.6489-1.68260.20221430.14751736X-RAY DIFFRACTION100
1.6826-1.71920.20251410.14841739X-RAY DIFFRACTION98
1.7192-1.75920.17461420.1411760X-RAY DIFFRACTION100
1.7592-1.80320.21621400.14791749X-RAY DIFFRACTION99
1.8032-1.85190.16451340.13831760X-RAY DIFFRACTION100
1.8519-1.90640.19351430.14221733X-RAY DIFFRACTION99
1.9064-1.96790.16441440.1421752X-RAY DIFFRACTION100
1.9679-2.03830.17891380.14611761X-RAY DIFFRACTION100
2.0383-2.11990.16991420.14781770X-RAY DIFFRACTION100
2.1199-2.21630.17441310.14551764X-RAY DIFFRACTION100
2.2163-2.33320.21021480.14531747X-RAY DIFFRACTION100
2.3332-2.47930.19631370.15761765X-RAY DIFFRACTION100
2.4793-2.67070.21691440.15931759X-RAY DIFFRACTION100
2.6707-2.93940.23991380.16921764X-RAY DIFFRACTION100
2.9394-3.36440.18991500.15911757X-RAY DIFFRACTION100
3.3644-4.23780.14221420.14261752X-RAY DIFFRACTION100
4.2378-36.49490.17751220.15531777X-RAY DIFFRACTION99

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