[English] 日本語
Yorodumi
- PDB-6e7e: High resolution crystal structure of IncA soluble domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e7e
TitleHigh resolution crystal structure of IncA soluble domain
ComponentsInclusion membrane protein A
KeywordsPROTEIN BINDING / membrane fusion / chlamydia / SNARE-like protein / inclusion
Function / homologypathogen-containing vacuole membrane / host cell membrane / extracellular region / membrane / Inclusion membrane protein A / Inclusion membrane protein A
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.12 Å
AuthorsCingolani, G. / Paumet, F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA56036 United States
National Institutes of Health/Office of the DirectorS10 OD017987 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI073486 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI116983 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA.
Authors: Cingolani, G. / McCauley, M. / Lobley, A. / Bryer, A.J. / Wesolowski, J. / Greco, D.L. / Lokareddy, R.K. / Ronzone, E. / Perilla, J.R. / Paumet, F.
History
DepositionJul 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inclusion membrane protein A


Theoretical massNumber of molelcules
Total (without water)19,5711
Polymers19,5711
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.323, 48.822, 41.738
Angle α, β, γ (deg.)90.00, 103.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Inclusion membrane protein A


Mass: 19571.092 Da / Num. of mol.: 1 / Fragment: soluble domain (UNP residues 87-246) / Mutation: V211A,V212A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: incA / Production host: Escherichia coli (E. coli) / References: UniProt: Q50FQ0, UniProt: P0CI27*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M sodium acetate trihydrate, pH 8.0, 20% w/v PEG3350
PH range: 6.0-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.12→15 Å / Num. obs: 52606 / % possible obs: 91.3 % / Redundancy: 7.3 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 47.9
Reflection shellResolution: 1.12→1.16 Å / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2307 / Rsym value: 0.298 / % possible all: 55

-
Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.12→14.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.021 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 2010 3.8 %RANDOM
Rwork0.141 ---
obs0.142 50533 90.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0.02 Å2
2---0.49 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.12→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 0 197 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131396
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171298
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.6341875
X-RAY DIFFRACTIONr_angle_other_deg1.6711.5763018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5565168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38522.56182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.611510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2391.281675
X-RAY DIFFRACTIONr_mcbond_other1.2231.28674
X-RAY DIFFRACTIONr_mcangle_it1.6881.933842
X-RAY DIFFRACTIONr_mcangle_other1.691.935843
X-RAY DIFFRACTIONr_scbond_it2.2711.759721
X-RAY DIFFRACTIONr_scbond_other2.2691.761722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7342.4911034
X-RAY DIFFRACTIONr_long_range_B_refined3.52317.8871706
X-RAY DIFFRACTIONr_long_range_B_other3.04316.6651640
X-RAY DIFFRACTIONr_rigid_bond_restr2.18932694
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.12→1.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 81 -
Rwork0.206 1971 -
obs--47.91 %

+
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