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- PDB-7tua: Human Synaptotagmin-1 C2B Y312F without Ca2+ -

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Basic information

Entry
Database: PDB / ID: 7tua
TitleHuman Synaptotagmin-1 C2B Y312F without Ca2+
ComponentsSynaptotagmin
KeywordsEXOCYTOSIS / C2 domain / AD3 / C2B / Greek Key / synaptotagmin
Function / homology
Function and homology information


chromaffin granule membrane / calcium-dependent phospholipid binding / synaptic vesicle membrane / calcium ion binding
Similarity search - Function
Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsDominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1R21MH070589-01 United States
Citation
Journal: To Be Published
Title: Human Synaptotagmin-1 C2B Y312F without Ca2+
Authors: Dominguez, M.J. / Karmakar, S. / Fuson, K.L. / Sutton, R.B.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
#2: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptotagmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9602
Polymers17,8641
Non-polymers961
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.440, 54.440, 104.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Synaptotagmin /


Mass: 17863.818 Da / Num. of mol.: 1 / Fragment: UNP Residues 269-419
Source method: isolated from a genetically manipulated source
Details: orginally cloned from human brain cDNA library / Source: (gene. exp.) Homo sapiens (human) / Tissue: brain / Gene: SYT1, hCG_2016754 / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J3KQA0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate pH 4.5,200 mM ammonium sulfate, 50% w/v PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.09717 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09717 Å / Relative weight: 1
ReflectionResolution: 1.35→34.69 Å / Num. obs: 39819 / % possible obs: 99.42 % / Redundancy: 13.7 % / Biso Wilson estimate: 16.57 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06954 / Rpim(I) all: 0.0176 / Rrim(I) all: 0.07183 / Net I/σ(I): 19.96
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 8.4 % / Rmerge(I) obs: 2.104 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 3769 / CC1/2: 0.383 / CC star: 0.744 / Rpim(I) all: 0.7573 / Rrim(I) all: 2.243 / % possible all: 95.14

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIX1.20_4459refinement
PDB-REDOrefinement
xia2data scaling
xia2data reduction
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tz3

6tz3


Resolution: 1.35→34.69 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 2003 5.04 %
Rwork0.1781 37755 -
obs0.1792 39758 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.32 Å2
Refinement stepCycle: LAST / Resolution: 1.35→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 5 153 1340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01291364
X-RAY DIFFRACTIONf_angle_d1.3431859
X-RAY DIFFRACTIONf_chiral_restr0.1011207
X-RAY DIFFRACTIONf_plane_restr0.0095241
X-RAY DIFFRACTIONf_dihedral_angle_d14.497537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.41681310.3592483X-RAY DIFFRACTION93.32
1.38-1.420.32481360.28482659X-RAY DIFFRACTION99.79
1.42-1.460.23691440.23522684X-RAY DIFFRACTION99.72
1.46-1.510.26631410.21312668X-RAY DIFFRACTION99.72
1.51-1.560.2031430.20082658X-RAY DIFFRACTION99.82
1.56-1.630.25541440.19942673X-RAY DIFFRACTION99.89
1.63-1.70.20141470.20992697X-RAY DIFFRACTION99.89
1.7-1.790.18581400.17322668X-RAY DIFFRACTION99.96
1.79-1.90.18341420.15142713X-RAY DIFFRACTION100
1.9-2.050.18361440.15342715X-RAY DIFFRACTION100
2.05-2.260.19711440.15462739X-RAY DIFFRACTION100
2.26-2.580.16531430.1562721X-RAY DIFFRACTION99.97
2.58-3.250.21211480.1832771X-RAY DIFFRACTION99.97
3.25-34.690.18431560.17422906X-RAY DIFFRACTION99.9

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