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

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Basic information

Entry
Database: PDB / ID: 1fvh
TitleCRYSTAL STRUCTURE ANALYSIS OF NEURONAL SEC1 FROM THE SQUID L. PEALEI
ComponentsSEC1
KeywordsENDOCYTOSIS/EXOCYTOSIS / PARALLEL BETA-SHEETS / LEFT-HAND TURN CONNECTION / HELICAL BUNDLE / 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: 2.8 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 1.3Aug 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

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Assembly

Deposited unit
A: SEC1


Theoretical massNumber of molelcules
Total (without water)67,8311
Polymers67,8311
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.125, 123.183, 63.891
Angle α, β, γ (deg.)90.00, 110.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SEC1


Mass: 67830.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Description: LOLIGO, PEALEI, GIANT AXON / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O62547
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.94 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 277 K / Method: batch crystallization / pH: 7.4
Details: Hepes, potassium chloride, dithiothreitol , pH 7.4, BATCH CRYSTALLIZATION, temperature 277K
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
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: ID14-1 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. all: 17776 / Num. obs: 16849 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 60.02 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1293 / % possible all: 72.6

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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: 2.8→14.91 Å / Rfactor Rfree error: 0.01 / 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
Rfree0.283 821 4.9 %RANDOM
Rwork0.2342 ---
all0.2366 17588 --
obs0.2366 16654 95.4 %-
Solvent computationSolvent model: flat model / Bsol: 34.6129 Å2 / ksol: 0.323526 e/Å3
Displacement parametersBiso mean: 61.74 Å2
Baniso -1Baniso -2Baniso -3
1--3.4 Å20 Å224.18 Å2
2---6.64 Å20 Å2
3---10.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.42 Å
Luzzati d res low-14.91 Å
Luzzati sigma a0.42 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 0 37 4449
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.46055
X-RAY DIFFRACTIONc_bond_d0.007562
X-RAY DIFFRACTIONc_dihedral_angle_d22.69893
X-RAY DIFFRACTIONc_improper_angle_d0.98254
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.562
X-RAY DIFFRACTIONc_scbond_it0.672
X-RAY DIFFRACTIONc_scangle_it1.152.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.388 77 5.7 %
Rwork0.41 1269 -
obs--75.3 %
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: 2.8 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.69893
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98254
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: 0.388 / % reflection Rfree: 5.7 % / Rfactor Rwork: 0.41 / Rfactor obs: 0.41

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