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- PDB-9v9a: Crystal structure of the periplasmic domain of CadF from Campylob... -

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Basic information

Entry
Database: PDB / ID: 9v9a
TitleCrystal structure of the periplasmic domain of CadF from Campylobacter jejuni in complex with glycine
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
GLYCINE / Outer membrane beta-barrel domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
B: Outer membrane beta-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2947
Polymers26,8562
Non-polymers4385
Water3,351186
1
A: Outer membrane beta-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6954
Polymers13,4281
Non-polymers2673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area6130 Å2
MethodPISA
2
B: Outer membrane beta-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5993
Polymers13,4281
Non-polymers1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.221, 48.699, 49.695
Angle α, β, γ (deg.)109.842, 98.783, 106.208
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 207 - 319 / Label seq-ID: 6 - 118

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 207 through 302 or (resid 303...AA
2(chain 'B' and (resid 207 through 208 or (resid 209...BB

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Components

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


Mass: 13427.897 Da / Num. of mol.: 2
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 4000, MES

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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: Feb 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 21017 / % possible obs: 95.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.15 Å2 / CC1/2: 0.994 / Net I/σ(I): 16.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 957 / CC1/2: 0.887 / % possible all: 86.1

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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: 1.75→26.18 Å / SU ML: 0.1556 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 21.2984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 1008 4.8 %
Rwork0.17 19995 -
obs0.1716 21003 94.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.67 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 25 186 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551816
X-RAY DIFFRACTIONf_angle_d0.78562443
X-RAY DIFFRACTIONf_chiral_restr0.053263
X-RAY DIFFRACTIONf_plane_restr0.0049328
X-RAY DIFFRACTIONf_dihedral_angle_d20.27451105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.850.21211350.18412532X-RAY DIFFRACTION83.79
1.85-1.960.23031290.18432909X-RAY DIFFRACTION94.97
1.96-2.110.27041580.16522893X-RAY DIFFRACTION95.73
2.11-2.330.21021460.16042879X-RAY DIFFRACTION96.4
2.33-2.660.19271610.16792906X-RAY DIFFRACTION96.57
2.66-3.350.18881420.17172918X-RAY DIFFRACTION96.02
3.35-26.180.19111370.16962958X-RAY DIFFRACTION97.54
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)
12.22573525352-0.506709175450.5872926170631.084570265411.348583056522.661920639240.0346599368241-0.0993703073446-0.05924533965620.197591374573-0.2001360746350.1711910902090.190233783434-0.2270273737060.1265266617520.192659259253-0.01768196983170.006124776015120.108801495484-0.005098412238930.1821870397665.55270113759-27.461748363317.3129511318
23.47810759461-0.6142476232151.812959685192.72741968863-0.04023266395415.48618557787-0.208085551994-0.5671574603950.07711396939170.536448148069-0.04910445176760.422876621782-0.138669475865-0.5512451693070.2066010434880.2218686106520.006387582077110.07487049475920.217678098025-0.07652744156860.2420109929894.87571109221-23.749003860528.3810309068
31.8407343772-0.1259700991380.5795677452760.9204893066050.7058995806243.02196318569-0.0864695010727-0.235565599368-0.05328253133730.313259970103-0.1133583650510.01246756648480.397788638209-0.2111368549090.01888544658920.208407520391-0.0246936940040.004299390550980.1217520155370.03592875164570.15653368133810.9977256023-33.65255474520.8545167547
40.936654323597-1.17272592503-1.297251216222.605622165243.500469036825.786431085240.0397779264322-0.06611521925490.0676216870132-0.09479826912710.139624890529-0.133566853247-0.2861396083270.221858642233-0.2260402467470.112519764797-0.0114504309377-0.0008980686138080.1144077889560.01373110956880.14772059683615.4838138153-27.798977349115.5529885196
50.8411840024510.2764408701280.3323379388851.37596796131.253582331141.560079658570.08377640650050.00297721358831-0.063022410260.2035877069380.0853949340613-0.1556803636410.2745574721110.0236351885166-0.1061734837490.148803645476-0.00405556875506-0.00356228530590.09817264371280.02194396166390.11818953246510.4539183098-33.80838454917.2890484343
63.232154923560.961451972299-0.7340492487322.638342321532.054756646452.39983046798-0.05764559637580.1755436680020.2368100081770.145277328434-0.08184590635010.1615991985570.0835024954523-0.07170554798250.1157282656410.130990820120.00475505942405-0.00919445782640.1356385228140.0122894373110.1770073583161.07325819359-31.7572719266.82367728375
72.13838127846-1.311849851712.490965340820.893593643442-1.019581550226.77598964395-0.0378590166339-0.405731479843-0.7293245545780.426270760874-0.112636053178-0.1119067791160.322527219421-0.0984148439024-0.09579893388170.284643582464-0.0714819456585-0.02367381385360.2425891147290.1335825764790.2428243062249.48638419087-35.171677774826.8041289778
81.63184753773-0.232248558827-0.8873520114473.116631261483.093283400238.235285390950.2753881659930.640633812445-0.400161513832-0.2995081112230.127515787175-0.1221477524990.1282913115340.58458971686-0.3813877341350.2129193713310.0799896327815-0.01163825826670.36237903984-0.07656606087040.2273518969983.22087250657-50.565947836417.0669529708
92.90852201674-0.7711259958132.682705595773.77388885201-3.445727862788.6127462658-0.0821569518339-0.1005775583670.08572471916990.4616544237940.190010114370.377182966367-0.680005558514-0.491168816791-0.1085081732560.2093214742270.04307694021070.01023129062730.126703151726-0.01376137923910.144993162226-6.96729611346-45.146778735831.4422980596
101.6016535319-0.0110513142072-0.4654215706673.678959705882.063484603863.476915518990.0680999792681-0.00394095315242-0.057039290798-0.02952657961880.0451230632738-0.212620986344-0.07385719850670.0679438011784-0.1335019753190.13506489583-0.01771746002-0.02614574106160.1560087226980.04034470420530.176695823333-3.47000559471-43.682971577214.0908432997
112.827354414940.1615996467940.5130013970672.78260261123-0.430256922398.007984272580.1026775378150.277221536051-0.193558783718-0.2470260527750.278194483607-0.01729241824980.826333768180.362071994256-0.2949747880570.1832983298490.0191360282814-0.009623330622930.180784089028-0.04873402514160.18891469465-3.62929421938-55.632035407512.4975202889
120.622793164952-0.3602238606260.4691551564151.37238446848-1.706638312314.374754781660.00125712396609-0.0961513428281-0.01530668818380.03639338272280.07907232598110.09247420943680.196132555111-0.224878005384-0.1380376627550.138636013672-0.007494216386830.008267409555860.133712725841-0.006969388530090.150534823362-9.21278659069-52.765853872928.2025018374
130.53884584104-0.01888080895160.5446816873211.25640029925-0.2457129574292.939890520950.1124312161830.129010956201-0.116004157097-0.006682939008810.02836629889020.06938190116090.5833436088830.388325283573-0.120858897330.1894591492590.04729898095380.009391106276390.166363538224-0.01877819486210.15128556844-2.51379077219-56.169410344325.7083226579
142.37532194742-2.129160693290.8202002907462.934620620830.3549956578132.00778193208-0.0869703585604-0.005876813708970.211730164683-0.00320650439233-0.0518694713699-0.208521446926-0.1300722935130.838795073317-0.003503309925930.1457871258690.0202501292139-0.002118729514280.2499934741720.01278498216880.155389985353.6273319094-48.893158302135.0201680321
151.72140306719-0.1000369015260.6723435650912.473906037612.189423228548.901787673870.1153062653560.0712466665976-0.406787651763-0.068227633426-0.05811630780520.1387879609460.7522548786210.37477492311-0.06582206877410.2296668020420.0389894069773-0.03644213177140.18818548106-0.02538272477440.213826655788-1.54644052984-55.846410162215.3534023939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 224 )
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 240 )
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 257 )
4X-RAY DIFFRACTION4chain 'A' and (resid 258 through 278 )
5X-RAY DIFFRACTION5chain 'A' and (resid 279 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 310 )
7X-RAY DIFFRACTION7chain 'A' and (resid 311 through 319 )
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 224 )
10X-RAY DIFFRACTION10chain 'B' and (resid 225 through 240 )
11X-RAY DIFFRACTION11chain 'B' and (resid 241 through 251 )
12X-RAY DIFFRACTION12chain 'B' and (resid 252 through 279 )
13X-RAY DIFFRACTION13chain 'B' and (resid 280 through 302 )
14X-RAY DIFFRACTION14chain 'B' and (resid 303 through 310 )
15X-RAY DIFFRACTION15chain 'B' and (resid 311 through 319 )

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