[English] 日本語
Yorodumi
- PDB-7rxu: Crystal structure of Cj1090c -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rxu
TitleCrystal structure of Cj1090c
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Bacterial lipoprotein / LPS / LptE / Outer membrane
Function / homologyLipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / outer membrane / Gram-negative-bacterium-type cell outer membrane assembly / Lipoprotein
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, Y. / Yeo, H.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationE-1616 United States
CitationJournal: Proteins / Year: 2023
Title: Crystal structure of Campylobacter jejuni lipoprotein Cj1090c.
Authors: Paek, S. / Kawai, F. / Venisetty, N. / Kim, Y. / Yeo, H.J.
History
DepositionAug 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5303
Polymers17,3761
Non-polymers1542
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.071, 89.071, 118.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

-
Components

#1: Protein Lipoprotein /


Mass: 17375.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: A4277_01250, A7M07_00410, A8118_01785, A8M99_00395, A9M03_02130, AZ817_04255, B5660_02510, B5946_02175, BBJ87_05465, BFD99_07545, BM409_03070, BWN12_01085, BZN49_00430, C1418_01685, C5M81_ ...Gene: A4277_01250, A7M07_00410, A8118_01785, A8M99_00395, A9M03_02130, AZ817_04255, B5660_02510, B5946_02175, BBJ87_05465, BFD99_07545, BM409_03070, BWN12_01085, BZN49_00430, C1418_01685, C5M81_04330, CAZ42_00395, CBW88_01330, CUT57_04850, CXE90_00065, D6H09_01620, DCB46_00240, DDV78_00275, DW573_04295, E5G70_01890, E7M04_02545, E7P31_00425, E8P01_00425, F0N28_01095, F1L44_00395, F1P05_04495, F1P94_03815, F3658_01355, F6069_04745, F6306_03525, F7843_04325, F7J55_02570, F7N67_01205, FM724_02000, FMI86_00510, FNW64_00425, FV854_00505, FW006_01825, FW073_02350, FW865_04530, FZ832_03995, FZ903_02320, GAU91_00760, GC764_01595, GHZ28_01110, GIF20_01850, GJO28_03750, GOY41_00395, GPY90_00420, GQ237_00185, GQV25_05720, GWF31_00500, GZ515_000638, GZ802_000127, YP14_03280
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1E7P3T3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, calcium acetate, glycerol, MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 11050 / % possible obs: 97.4 % / Redundancy: 14.4 % / Biso Wilson estimate: 67.63 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.4 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 11050

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→14.94 Å / SU ML: 0.2174 / Cross valid method: NONE / σ(F): 1.51 / Phase error: 23.495 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2368 528 4.78 %
Rwork0.1988 10509 -
obs0.2006 11037 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 10 4 1069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441089
X-RAY DIFFRACTIONf_angle_d0.57471467
X-RAY DIFFRACTIONf_chiral_restr0.0454165
X-RAY DIFFRACTIONf_plane_restr0.0034190
X-RAY DIFFRACTIONf_dihedral_angle_d8.8248903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.28931290.24582455X-RAY DIFFRACTION94.03
2.64-3.020.26011330.24652631X-RAY DIFFRACTION99.75
3.02-3.790.27811310.2152680X-RAY DIFFRACTION99.68
3.79-14.940.20851350.17792743X-RAY DIFFRACTION96.51
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)
15.667292364893.416945957011.515882733028.265442043750.1941065703875.37472330863-0.137648782329-0.2318502407110.2699747760150.5428891238670.152255597133-0.278344884834-0.810941344286-0.7738944869120.2199849408690.6593416179290.303368270654-0.002925233148870.6087932107070.01775028124580.49684979105336.06036582078.6962370157517.9294506817
24.938227138347.065529780660.8279648329654.731473979851.667058026182.256438694060.128222737327-0.00755822667180.2493047887610.3981180543950.2044354344450.387126889859-0.293093073696-0.145952317165-0.3182696689940.7840646017530.2898870309740.08746863774880.623083182885-0.03457249393920.66081974176640.69388594417.5303335418117.4601701088
38.04031778513-2.964446493791.557604138671.61108614059-2.482976152929.99308329952-1.274116840071.2703040318-0.03525007485220.5123881319870.208055754872-3.22711376251-2.175365857172.177884054620.5954158867371.50136045812-0.22018405857-0.2373344279441.244438280490.0669860540781.3673031933855.451066702617.884221055225.6653147435
44.04673191482-0.4234884605661.337288439275.922780802060.8640827344467.04787239896-0.17645299481-0.7793513426410.4603001497871.253990545370.0932008404579-0.0252274188789-0.232724427333-0.1169103915370.07183016360750.9533702086180.30109594114-0.02494659872050.738315080279-0.06567124145660.67788255856743.34789701547.5217861524829.2683388513
55.447817903743.75708873512.563623088474.602441081771.908504848747.066780274550.0335567768960.02702509509520.3114416615990.612107275151-0.222337914360.42855833804-0.175642365356-1.514585000190.3575804044190.6337311161110.2900636040470.07891172454670.857361339631-0.034595861040.57710362378730.90234425927.3307547170516.2270887437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 32 )
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 110 )

+
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