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- PDB-7rxu: Crystal structure of Cj1090c -

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Basic information

Entry
Database: PDB / ID: 7rxu
TitleCrystal structure of Cj1090c
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Bacterial lipoprotein / LPS / LptE / Outer membrane
Function / homologyLPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / outer membrane / Gram-negative-bacterium-type cell outer membrane assembly / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


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

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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: 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

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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

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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 )

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