[English] 日本語
Yorodumi
- PDB-9v99: Crystal structure of the periplasmic domain of CadF from Campylob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v99
TitleCrystal structure of the periplasmic domain of CadF from Campylobacter jejuni in complex with a peptidoglycan peptide
Components
  • API-DAL-DAL
  • Outer 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
2,6-DIAMINOPIMELIC ACID / polypeptide(D) / Outer membrane beta-barrel domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane beta-barrel domain-containing protein
B: Outer membrane beta-barrel domain-containing protein
I: API-DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3784
Polymers27,1883
Non-polymers1901
Water1,946108
1
A: Outer membrane beta-barrel domain-containing protein
I: API-DAL-DAL


Theoretical massNumber of molelcules
Total (without water)13,7602
Polymers13,7602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane beta-barrel domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6182
Polymers13,4281
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.855, 49.226, 55.981
Angle α, β, γ (deg.)90.000, 112.062, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 206 - 319 / Label seq-ID: 5 - 118

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 206 through 219 or (resid 220...AA
22(chain 'B' and (resid 206 through 286 or (resid 287...BB

-
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: Polypeptide(D) API-DAL-DAL


Mass: 332.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-API / 2,6-DIAMINOPIMELIC ACID


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 2000, Hepes

-
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: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 20881 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.31 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1050 / CC1/2: 0.785 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.39 Å / SU ML: 0.2435 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 1043 5.08 %
Rwork0.2066 19476 -
obs0.2082 20519 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 5 108 1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061845
X-RAY DIFFRACTIONf_angle_d0.77312481
X-RAY DIFFRACTIONf_chiral_restr0.0535270
X-RAY DIFFRACTIONf_plane_restr0.0049337
X-RAY DIFFRACTIONf_dihedral_angle_d27.8523702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.890.33691570.29712759X-RAY DIFFRACTION99.02
1.89-2.010.28481700.25012735X-RAY DIFFRACTION99.38
2.01-2.170.25631490.22292758X-RAY DIFFRACTION99.49
2.17-2.390.25571100.20162811X-RAY DIFFRACTION99.62
2.39-2.730.28161520.21042807X-RAY DIFFRACTION99.63
2.73-3.440.21351420.19612790X-RAY DIFFRACTION99.39
3.44-27.390.19511630.18422816X-RAY DIFFRACTION98.51
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)
15.82159541305-0.4193800895442.085388748211.830025908270.652934742764.25751772402-0.009248368170.4190523898930.100905356128-0.186058116631-0.00107802027594-0.103552852636-0.0102140945850.02701235304440.009398324864640.14285492261-0.01602126668490.03784745944230.1276129164480.04144779581960.17238119182316.9534053523-13.931397478721.0122927211
28.006453391426.867420811143.94854570086.89361542183.881257934085.02493246827-0.1051662283960.2837177059820.986053109532-0.585909997844-0.1935823449570.368864218505-0.434231064948-0.1920632795710.3122659686230.2335632522330.08830256551020.05065729130880.1945308617680.07700872563110.2734191572798.27838807517-9.2309024625117.0337201919
38.09895544795-0.310595911156.065609175472.04184511731-0.7377853498797.249170681640.1540204297-0.0980764615137-0.97272127211-0.1277323925560.1993575364420.1878921115220.136809181536-0.335652042229-0.3508292246560.132496725469-0.01175660114390.02248289456720.0862881736598-0.02903432999090.20645301272212.430834829-20.783181526622.8254104962
47.76818837715-6.003698652686.792639462436.42131525307-5.480401070656.38090246509-0.0817162394642-0.2946058256-0.02006594949620.1551038452970.1791211816510.250366788135-0.00787014086389-0.225463908361-0.09471349797670.123313509275-0.007918390619020.04722062015370.134323731029-0.0007325439707990.15483816286114.7192309088-16.338299749731.2441727221
54.56610421808-2.006826040971.644355765613.1854770785-0.1858183077211.20659032780.0876288471293-0.07674008653-0.560976338959-0.0109247238452-0.0142426779240.3221303806520.045938039116-0.089001487101-0.06974206496960.135513885017-0.02493591968430.02413363542210.12013082025-0.005382433409040.14769115128115.8042144848-20.536345861924.5963524212
67.20174709217-0.6897343362582.451974104452.354412224811.122870749813.26039871093-0.05478841899550.266220489671-0.00405212162528-0.150645545154-0.0212620991061-0.0304353632509-0.0754087626197-0.003794165790490.06250849250810.1349636064590.01190375179370.03323512840760.09450937916120.01792761201810.16774969697218.5155984024-19.199274114120.4701668126
74.92878651807-0.6263025320871.507996909684.52738509065-2.029742837043.839931111840.195465941729-0.25230532505-0.1171647526240.0474211780826-0.04201184780240.3248616181230.11936182053-0.00711372376067-0.1702984842010.190613700673-0.02019497866330.01185070327120.150681145988-0.002461104717230.30603843963716.36857099490.125470838854.7184122479
88.99906119908-6.275646999743.55625602155.43166324601-2.773109681743.00655335314-0.177562196154-0.3246008834920.7870922001680.646559421359-0.0590617369424-0.378916145233-0.4189743146180.1689133838250.2380452612960.243465284977-0.0906276748641-0.01391476106790.193616025842-0.03989379988960.30917642792624.86887632984.675945026518.98649414883
98.283985840832.189287094765.002137195932.633187574281.26023548845.542454936270.564822449675-0.32200466968-0.940443783365-0.02979065700190.0227021250517-0.06453471733140.285631531074-0.0643341522187-0.5940339493870.134376106811-0.01305920381160.01298025427010.1132121370440.00336427100950.31748429079420.2092819192-6.507128578912.07016177999
102.012256582872.001603376438.812616618292.014819225287.036294175157.92534126789-0.2849364958770.6283292133880.014457188105-0.3915212896040.223883345256-0.0968442617931-0.2706085117920.2893613335780.04902992480320.206709018939-0.02889736094050.02919836145540.219861786082-0.002353410819940.20606820797518.4763404241-1.37739490294-5.64105577845
113.799258222971.516221158012.351800553740.7341949528441.123447307471.735346815250.2377204630090.321020966766-0.88530409861-0.1186569818270.0924538369467-0.970877431651-0.0505130585360.256817616035-0.312675103560.161293014757-0.01290040324370.05842543231310.228398208682-0.0558229057210.43044510335129.697093107-2.299447598760.494844538091
125.71250055393-0.7122713162020.7271144856910.692870920112-0.7609693503093.5677847072-0.0136652918224-0.0699215224465-0.2153567387970.1339721144350.07105761711950.768971664999-0.0485105536362-0.326059103984-0.06333749421450.1785321263660.00365300609510.01420027214590.1629971714060.006715970402090.5070778418875.18426449568-6.58724006071.37222019984
131.734237016080.835399377903-1.237717236962.37214073942-0.4591873909782.77673613813-0.0672054261815-0.276669250022-0.9559908772610.389778386798-0.177029819907-0.1228874146180.1543236376290.05957859464210.2426108498230.200717217159-0.0355449517008-0.008763514466820.1562723966310.05230832974610.44579311290124.4215645695-7.396272488086.56400742961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 206 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 319 )
7X-RAY DIFFRACTION7chain 'B' and (resid 206 through 224 )
8X-RAY DIFFRACTION8chain 'B' and (resid 225 through 240 )
9X-RAY DIFFRACTION9chain 'B' and (resid 241 through 257 )
10X-RAY DIFFRACTION10chain 'B' and (resid 258 through 278 )
11X-RAY DIFFRACTION11chain 'B' and (resid 279 through 290 )
12X-RAY DIFFRACTION12chain 'B' and (resid 291 through 310 )
13X-RAY DIFFRACTION13chain 'B' and (resid 311 through 319 )

+
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