[English] 日本語
Yorodumi
- PDB-1s94: Crystal structure of the Habc domain of neuronal syntaxin from th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s94
TitleCrystal structure of the Habc domain of neuronal syntaxin from the squid Loligo pealei
Componentss-syntaxin
KeywordsENDOCYTOSIS/EXOCYTOSIS / three helix bundle / structural plasticity / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


SNAP receptor activity / vesicle-mediated transport / intracellular protein transport / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesLoligo pealei (longfin inshore squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsBracher, A. / Weissenhorn, W.
CitationJournal: BMC STRUCT.BIOL. / Year: 2004
Title: Crystal structure of the Habc domain of neuronal syntaxin from the squid Loligo pealei reveals conformational plasticity at its C-terminus
Authors: Bracher, A. / Weissenhorn, W.
History
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: s-syntaxin
B: s-syntaxin


Theoretical massNumber of molelcules
Total (without water)41,4302
Polymers41,4302
Non-polymers00
Water0
1
A: s-syntaxin


Theoretical massNumber of molelcules
Total (without water)20,7151
Polymers20,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: s-syntaxin


Theoretical massNumber of molelcules
Total (without water)20,7151
Polymers20,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.056, 73.056, 224.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein s-syntaxin


Mass: 20715.221 Da / Num. of mol.: 2 / Fragment: Habc domain / Mutation: M1R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo pealei (longfin inshore squid) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 pUBS / References: UniProt: O46345

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 400, 0.2M Na-citrate, 0.1M Tris HCl, 20mM HEPES-KOH, 100mM KCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0088 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 3.3→15 Å / Num. all: 9361 / Num. obs: 9304 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.8
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 4.6 / Num. unique all: 906 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1EZ3, chain A

1ez3


Resolution: 3.34→14.97 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.818 / SU B: 25.633 / SU ML: 0.43 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.889 / ESU R Free: 0.55 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37537 500 5.4 %RANDOM
Rwork0.30878 ---
obs0.31255 8751 100 %-
all-8751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.344 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2---1.79 Å20 Å2
3---3.57 Å2
Refinement stepCycle: LAST / Resolution: 3.34→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 0 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211634
X-RAY DIFFRACTIONr_bond_other_d0.0020.021456
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9452216
X-RAY DIFFRACTIONr_angle_other_deg0.95933290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365222
X-RAY DIFFRACTIONr_chiral_restr0.0830.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021881
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
X-RAY DIFFRACTIONr_nbd_refined0.3150.2564
X-RAY DIFFRACTIONr_nbd_other0.2540.21920
X-RAY DIFFRACTIONr_nbtor_other0.090.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.228
X-RAY DIFFRACTIONr_mcbond_it0.6841.51130
X-RAY DIFFRACTIONr_mcangle_it1.32821762
X-RAY DIFFRACTIONr_scbond_it1.843504
X-RAY DIFFRACTIONr_scangle_it3.4784.5454
LS refinement shellResolution: 3.34→3.421 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.5 33
Rwork0.413 575
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2393-0.8554-2.19012.06295.428711.5022-0.32380.09030.1133-0.3332-0.10080.2081-0.61440.30190.42460.16690.0249-0.09180.3886-0.09520.237956.448960.432936.5746
21.2178-0.7459-1.706118.864414.125611.7314-0.2142-0.2344-0.15020.1301-0.07650.44380.0244-0.13540.29080.14450.0504-0.03620.3701-0.12830.12449.782955.46437.4181
30.02190.93730.31440.20140.26711.3654-0.0199-0.0556-0.03070.14370.202-0.10540.21470.2549-0.18210.26660.0451-0.05150.3664-0.11480.23759.806352.583442.0149
43.18830.64322.1352-0.34920.65252.3849-0.0050.10920.33470.0738-0.2657-0.10710.1131-0.01930.27070.31380.0333-0.16190.112-0.07190.19480.569669.928976.4091
57.77320.4384.8272-0.10060.91523.91720.34010.2140.68270.4155-0.57970.20890.5213-0.03810.23950.28930.0565-0.18290.2002-0.03850.115773.482474.526880.7975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 6636 - 71
2X-RAY DIFFRACTION2AA74 - 10779 - 112
3X-RAY DIFFRACTION3AA113 - 151118 - 156
4X-RAY DIFFRACTION4BB32 - 10537 - 110
5X-RAY DIFFRACTION5BB113 - 156118 - 161

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more