[English] 日本語
Yorodumi
- PDB-2fgs: Crystal structure of Campylobacter jejuni YCEI protein, structura... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2fgs
TitleCrystal structure of Campylobacter jejuni YCEI protein, structural genomics
ComponentsPutative periplasmic protein
KeywordsLIPID BINDING PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Periplasmic protein / :
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Campylobacter Jejuni YceI Periplasmic Protein
Authors: Patskovsky, Y. / Ramagopal, U. / Almo, S.C.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1652
Polymers20,0691
Non-polymers961
Water00
1
A: Putative periplasmic protein
hetero molecules

A: Putative periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3294
Polymers40,1372
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_556-x,-x+y,-z+11
Unit cell
Length a, b, c (Å)179.535, 179.535, 50.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
DetailsThe biological assembly is a homodimer. The second part of the assembly is generated by the two-fold axis -x, y-x, 1-z

-
Components

#1: Protein Putative periplasmic protein


Mass: 20068.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: Cj0420 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9PI85, UniProt: Q79JB5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.1 Å3/Da / Density % sol: 78.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.2M AMMONIUM SULFATE, 0.1M BIS-TRIS, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 19, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 11129 / Num. obs: 11129 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.124 / Rsym value: 0.088 / Net I/σ(I): 6.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1092 / Rsym value: 0.46 / % possible all: 100

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y0G

1y0g


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.635 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.364 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS UNIDENTIFIED DENSITY WAS FOUND IN THE CENTRAL CAVITY OF THE PROTEIN BUT THE STRUCTURE OF THE BOUND LIGAND HAS NOT BEEN DETERMINED YET
RfactorNum. reflection% reflectionSelection details
Rfree0.27986 531 4.8 %RANDOM
Rwork0.24314 ---
all0.262 10524 --
obs0.24492 10524 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.73 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å21.82 Å20 Å2
2--3.65 Å20 Å2
3----5.47 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 5 0 1333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221350
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9621809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.18326.55761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.92515268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg36.512152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02978
X-RAY DIFFRACTIONr_nbd_refined0.190.3452
X-RAY DIFFRACTIONr_nbtor_refined0.3060.5918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.574
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.369
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.522
X-RAY DIFFRACTIONr_mcbond_it1.5752851
X-RAY DIFFRACTIONr_mcangle_it2.97731348
X-RAY DIFFRACTIONr_scbond_it4.5374541
X-RAY DIFFRACTIONr_scangle_it7.1646461
LS refinement shellResolution: 2.9→2.974 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 39 -
Rwork0.359 751 -
obs-790 100 %

+
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