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- PDB-9v9b: Crystal structure of the periplasmic domain of Campylobacter jeju... -

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Basic information

Entry
Database: PDB / ID: 9v9b
TitleCrystal structure of the periplasmic domain of Campylobacter jejuni CadF R268E
ComponentsOuter membrane beta-barrel domain-containing protein
KeywordsPEPTIDE BINDING PROTEIN / CadF / Campylobacter jejuni / peptidoglycan
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane beta-barrel protein, Proteobacteria / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA family / OmpA-like domain ...Outer membrane beta-barrel protein, Proteobacteria / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA family / OmpA-like domain / OmpA-like domain superfamily / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane beta-barrel domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOh, H.B. / Yoon, S.I.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00208153 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2025
Title: Crystal structures of Campylobacter jejuni CadF reveal a potential role for the arginine residue R268 in peptidoglycan recognition and pocket formation.
Authors: Oh, H.B. / Yoon, S.I.
History
DepositionMay 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane beta-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5923
Polymers13,4001
Non-polymers1922
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-20 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.666, 76.055, 30.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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Components

#1: Protein Outer membrane beta-barrel domain-containing protein / CadF


Mass: 13399.817 Da / Num. of mol.: 1 / Mutation: R268E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: C3H42_04770, C3H48_01715, C3H57_06665 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E7NJR0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 17521 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 11.08 Å2 / CC1/2: 0.993 / Net I/σ(I): 16.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 864 / CC1/2: 0.858 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.95 Å / SU ML: 0.0917 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1786 865 4.95 %
Rwork0.1672 16613 -
obs0.1678 17478 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.31 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 10 116 1011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049905
X-RAY DIFFRACTIONf_angle_d0.7761220
X-RAY DIFFRACTIONf_chiral_restr0.0508132
X-RAY DIFFRACTIONf_plane_restr0.0046163
X-RAY DIFFRACTIONf_dihedral_angle_d13.1149550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.60.23051420.20792694X-RAY DIFFRACTION98.88
1.6-1.720.18721240.18812742X-RAY DIFFRACTION99.9
1.72-1.890.18471460.16692721X-RAY DIFFRACTION99.93
1.89-2.160.16561470.15092754X-RAY DIFFRACTION100
2.16-2.730.16991580.16322775X-RAY DIFFRACTION100
2.73-28.950.17631480.16442927X-RAY DIFFRACTION99.74
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)
16.2679852853-3.022087576394.360017335597.52966679933-4.856715564118.51506055875-0.0542001872197-0.4185132567990.05168226966050.5342427392850.1540176469230.276951569291-0.206343710459-0.141896490753-0.008872106628160.14217481783-0.007669678775470.004292208561960.1008696632750.001040073210250.1435593770924.167915353212.8878917702-1.82676292003
21.02573971094-0.9931261113981.868018083955.74453288377-3.998862075974.83152603354-0.00936910081346-0.04299694484560.09058590473050.0846841792477-0.04807021891950.105533626595-0.1741552691550.00260848616908-0.02738982487850.05913754866960.01154984064320.02342664322710.0877205342469-0.00250178152680.076579269730520.181275803322.5746481387-14.1986709446
38.71951311883-6.10120978960.264030180514.29365844167-0.1832768718471.58778789559-0.1240487687070.01745503309630.381213730460.08701608235680.0162870747115-0.272713495115-0.1863097356540.007047208391740.1031050640930.112193086703-0.02438841576050.0002275178253320.0841355168974-0.01355929676760.11098066161131.105253289118.4639910534-5.07226846838
42.59252470858-0.0125841888052-0.2650445292150.3942872849450.02640767470090.2708958945860.0251508834574-0.189609437668-0.1155008655990.00292350056805-0.000527477913721-0.0083847121172-0.0141626138165-0.0434030914708-0.05094298029280.0749724821823-0.002776733500670.0005218280649640.06539945090930.002598394443490.075266642741722.66501369177.21144524174-7.92146883011
57.009866891543.612634630530.5261491758313.47399564610.3347991141450.729583985155-0.1229879382890.2669657663690.0459736039605-0.1867038567410.0938971863490.03715435103340.0169911854-0.04670020553250.04164300307180.1031011050110.00910975595225-0.003815446090230.07539083252290.01785040881030.054273408056719.685642473210.3134739397-15.9002193117
66.241135643870.0803056098905-0.4181098567820.7743516298530.03100372820711.35628374656-0.07099759875990.183197302859-0.0214778523739-0.03516791777950.0617354303890.0501754192555-0.04257886785780.05175070876340.0194880228510.0761566901120.000105798053254-0.001554048666270.0603292995369-0.001856096538620.066526461382132.10479452368.56341633874-12.748962453
75.48875049487-1.60328586994-1.390272119351.804151495431.363227449411.90922229391-0.0322398074013-0.173584006842-0.0924009205490.06152697599890.04190999781690.05386220724890.0763148017630.0156236659102-0.01647060511570.0642901396587-0.00460458483744-0.01135734807070.05432472692720.01904840300520.05210472784248.5099757790210.5598310849-4.54827423958
86.97029638999-3.569862641343.031539735324.88457658822-0.9926992538132.9855757267-0.0497968059694-0.0344539963816-0.1024695501550.1464687063760.0342198714914-0.05085877444240.01943464762350.02294107435740.01623336199190.0694281580444-0.02107780777160.02335596537630.07338516777170.01241703071720.074149190201427.72483313046.08599492193-4.65822698447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 213 )
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 224 )
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 240 )
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 257 )
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 290 )
7X-RAY DIFFRACTION7chain 'A' and (resid 291 through 310 )
8X-RAY DIFFRACTION8chain 'A' and (resid 311 through 319 )

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