3F00

Crystal Structure of Synaptotagmin I C2A domain with Cu(II)

• PDB DOI: https://doi.org/10.2210/pdb3F00/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-10-24 Released: 2009-09-08 
• Deposition Author(s): Guo, F., Dakshinamurthy, R., Thallapuranam, S.K.K., Sakon, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.244 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Crystal structure of Synaptotagmin I C2A

Guo, F., Dakshinamurthy, R., Thallapuranam, S.K.K., Sakon, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.27 kDa 
• Atom Count: 1,422 
• Modelled Residue Count: 143 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-1	A	143	Homo sapiens	Mutation(s): 0  Gene Names: SYT1, SVP65, SYT Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens) Explore P21579  Go to UniProtKB:  P21579
PHAROS:  P21579 GTEx:  ENSG00000067715

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHO	A	L-PEPTIDE LINKING	C5 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.244 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.647	α = 90
b = 38.363	β = 98.37
c = 44.016	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Guo, F., Dakshinamurthy, R., Thallapuranam, S.K.K., Sakon, J.

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2017-11-08
  Changes: Structure summary
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary