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- PDB-1fvf: CRYSTAL STRUCTURE ANALYSIS OF NEURONAL SEC1 FROM THE SQUID L. PEALEI -

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Basic information

Entry
Database: PDB / ID: 1fvf
TitleCRYSTAL STRUCTURE ANALYSIS OF NEURONAL SEC1 FROM THE SQUID L. PEALEI
ComponentsSEC1
KeywordsENDOCYTOSIS/EXOCYTOSIS / PARALLEL BETA-SHEETS / LEFT-HAND TURN CONNECTION / HELICAL BUNDLE / DIMER / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


vesicle-mediated transport
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesLoligo pealei (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBracher, A. / Weissenhorn, W.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structures of neuronal squid Sec1 implicate inter-domain hinge movement in the release of t-SNAREs.
Authors: Bracher, A. / Weissenhorn, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-ray Analysis of Squid Neuronal Sec1
Authors: Bracher, A. / Dresbach, T. / Betz, H. / Weissenhorn, W.
#2: Journal: Structure / Year: 2000
Title: The X-ray Crystal Structure of Neuronal Sec1 from Squid Sheds New Light on the Role of this Protein in Exocytosis
Authors: Bracher, A. / Perrakis, A. / Dresbach, T. / Betz, H. / Weissenhorn, W.
History
DepositionSep 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Derived calculations
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEC1
B: SEC1


Theoretical massNumber of molelcules
Total (without water)135,6612
Polymers135,6612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-27 kcal/mol
Surface area48150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.517, 118.517, 192.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96595, -0.09362, -0.24119), (-0.0495, -0.84814, 0.52746), (-0.25395, 0.52144, 0.81462)132.54146, 46.44696, 4.41443
2given(-0.96793, -0.08897, -0.23495), (-0.08135, -0.77383, 0.62815), (-0.2377, 0.62712, 0.74177)131.66405, 37.52565, 9.33096
DetailsThe dimer in the asymmetric unit represents the biological assembly.

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Components

#1: Protein SEC1


Mass: 67830.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Cell: GIANT AXON / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O62547

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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: 2.87 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG-1000, ammonium sulfate, sodium citrate, DTT, calcium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Bracher, A., (2000) Acta Crystallogr., Sect.D, 56, 501.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %(w/v)PEG10001reservoir
20.4 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir
420 mMdithiothreitol1reservoir
510 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.784
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.784 Å / Relative weight: 1
ReflectionResolution: 3.2→12 Å / Num. all: 25919 / Num. obs: 24825 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 82.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.8
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2449 / % possible all: 95.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EPU

1epu


Resolution: 3.2→12 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood function
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 1202 4.9 %RANDOM
Rwork0.2426 ---
all0.2449 26441 --
obs0.2449 24771 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.3616 Å2 / ksol: 0.318054 e/Å3
Displacement parametersBiso mean: 67.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å217.63 Å20 Å2
2--1.16 Å20 Å2
3----2.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.46 Å
Luzzati d res low-12 Å
Luzzati sigma a0.51 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8786 0 0 0 8786
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.39734
X-RAY DIFFRACTIONc_bond_d0.008096
X-RAY DIFFRACTIONc_dihedral_angle_d21.93185
X-RAY DIFFRACTIONc_improper_angle_d0.85466
X-RAY DIFFRACTIONc_mcbond_it2.141.5
X-RAY DIFFRACTIONc_mcangle_it3.762
X-RAY DIFFRACTIONc_scbond_it2.732
X-RAY DIFFRACTIONc_scangle_it4.452.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 3.2→3.31 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.407 143 5.8 %
Rwork0.37 2338 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 67.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.93185
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85466
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.407 / % reflection Rfree: 5.8 % / Rfactor Rwork: 0.37 / Rfactor obs: 0.37

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