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- PDB-12aj: Citrobacter rodentium contact dependent growth inhibition (CDI) t... -

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Basic information

Entry
Database: PDB / ID: 12aj
TitleCitrobacter rodentium contact dependent growth inhibition (CDI) toxin (CdiA-CT) in complex with E. coli GyrB
Components
  • Contact-dependent inhibitor A
  • DNA gyrase subunit B
KeywordsTOXIN / PROTEIN BINDING / Peptidase
Function / homology
Function and homology information


catalytic activity / toxin activity
Similarity search - Function
Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Pectin lyase fold / Pectin lyase fold/virulence factor / BRCT domain profile. / BRCT domain
Similarity search - Domain/homology
Fimbrial usher protein StbD / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Citrobacter rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCuthbert, B.J. / Hardy, C.D. / Kennady, J.R. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains
Authors: Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.
History
DepositionMar 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA gyrase subunit B
A: Contact-dependent inhibitor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9819
Polymers43,3362
Non-polymers6457
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-20 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.445, 64.955, 70.154
Angle α, β, γ (deg.)90.000, 101.692, 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

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Components

#1: Protein DNA gyrase subunit B


Mass: 25390.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gyrB, HVW04_15435 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7D7JXT0, DNA topoisomerase (ATP-hydrolysing)
#2: Protein Contact-dependent inhibitor A


Mass: 17945.842 Da / Num. of mol.: 1 / Mutation: C183A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (bacteria) / Gene: stbD, E2R62_11320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482PFX0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.88 Å3/Da / Density % sol: 34.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 5.5, 25% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 11, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35.69 Å / Num. obs: 21456 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Rrim(I) all: 0.057 / Χ2: 0.76 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1456 / CC1/2: 0.977 / Rpim(I) all: 0.144 / Rrim(I) all: 0.216 / Χ2: 0.46 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35.69 Å / SU ML: 0.1936 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.3343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 2144 10.01 %
Rwork0.1746 19267 -
obs0.1786 21411 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.72 Å2
Refinement stepCycle: LAST / Resolution: 2→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 42 131 2728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522684
X-RAY DIFFRACTIONf_angle_d0.65923641
X-RAY DIFFRACTIONf_chiral_restr0.0541399
X-RAY DIFFRACTIONf_plane_restr0.006473
X-RAY DIFFRACTIONf_dihedral_angle_d16.3012941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.24191300.19221171X-RAY DIFFRACTION90.28
2.04-2.090.29771510.19691252X-RAY DIFFRACTION97.63
2.09-2.150.23871360.20281321X-RAY DIFFRACTION99.05
2.15-2.210.24231460.19151269X-RAY DIFFRACTION98.54
2.21-2.290.20541360.18111297X-RAY DIFFRACTION98.9
2.29-2.370.2591470.19061279X-RAY DIFFRACTION99.03
2.37-2.460.25131470.18591291X-RAY DIFFRACTION98.49
2.46-2.570.1981350.19831285X-RAY DIFFRACTION96.53
2.57-2.710.2391410.18471275X-RAY DIFFRACTION99.02
2.71-2.880.21851520.18851303X-RAY DIFFRACTION99.59
2.88-3.10.21451400.18951314X-RAY DIFFRACTION99.18
3.1-3.410.23231410.17171285X-RAY DIFFRACTION98.48
3.41-3.910.19271400.15711285X-RAY DIFFRACTION96.81
3.91-4.920.17641460.14211315X-RAY DIFFRACTION99.52
4.92-35.690.20911560.18231325X-RAY DIFFRACTION98.01
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)
12.847764120860.2806352165512.874886831132.216735785241.796405666376.488293256530.1815715955180.0180278676645-0.06041672618320.39713006364-0.1598898509710.201672208760.486567553522-0.0674242768750.04536159349960.249018812315-0.003273973697630.01888117004860.1782548604350.006279398085070.2738485787158.064-11.89325.007
22.26224788203-0.06109938760281.169206261343.41802349836-0.5698300228691.683569406280.01909090880940.4800707275150.0552881515812-0.424811621638-0.101404579888-0.229988602553-0.0529020512880.2267897475570.07607588667280.2442206204260.0382904391140.03739766056270.280637580740.01269017272650.22706366620511.1466.39420.934
36.66120266095-0.118908528099-3.398003773890.3452137845231.276906200655.74692241480.3299943283410.2240903543490.663288437322-0.1815848255360.486364083582-0.763725832528-0.7529760001160.769146472177-0.4744154128480.312607488074-0.0887201928247-0.007807537746580.356139774135-0.05836107786140.36873537223314.709-3.4712.875
42.15627616208-0.07074777690280.2703631436152.749265367440.5525586148451.81140567810.04439605232140.07421376423920.02864033826390.00246032638931-0.01062491559420.285275953052-0.0549120658693-0.168222202271-0.02975009965420.1637460684890.007924452435780.005429262732680.180439784217-0.01403692075690.2067001734783.4425.66824.409
54.434461977070.327412839486-2.186993689252.408469893660.2264325197684.259541339570.0552739726302-0.05623457303130.1298120868820.146027718191-0.00626008612968-0.287919012898-0.1922828355420.368468515046-0.05722082252490.209878742656-0.00330053153937-0.03746263988090.184357983808-0.01229495108910.2517034999921.1611.49133.328
61.978377404060.0603944150783-0.2566702108491.73910040381-0.3946145538443.57979996123-0.1419994806560.788931982355-0.0590196238936-0.9707187962790.313492244287-0.2735695073720.4310506669020.1298872489610.003155334526680.498426184279-0.1289966358060.04100491514080.506742599932-0.05310379674060.27867738758411.726-14.834-4.31
72.36480349875-0.0468030158812-0.7702651910232.37787312559-1.01756940632.40467496469-0.09340077760420.151326100276-0.162254982997-0.3987865869350.1617705522670.118427076280.2815582557580.0194768910294-0.06138238237760.291608667092-0.0640926597176-0.008288669598370.311468497749-0.0617801089650.2228355817048.056-14.9857.156
82.94305227342-0.723718267269-1.033166895592.70809515527-0.6612964830863.4625596729-0.3096380022860.399559674419-0.595140038966-0.403113555562-0.0799873997345-0.03886200102441.353496781110.3700770523750.2171867839710.5355293886620.0462978537510.06645302236170.391730797142-0.1265167957930.2710752973314.973-23.2229.332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 11:34 )B11 - 34
2X-RAY DIFFRACTION2( CHAIN B AND RESID 35:97 )B35 - 97
3X-RAY DIFFRACTION3( CHAIN B AND RESID 98:120 )B98 - 120
4X-RAY DIFFRACTION4( CHAIN B AND RESID 121:184 )B121 - 184
5X-RAY DIFFRACTION5( CHAIN B AND RESID 185:219 )B185 - 219
6X-RAY DIFFRACTION6( CHAIN A AND RESID 181:202 )A181 - 202
7X-RAY DIFFRACTION7( CHAIN A AND RESID 203:262 )A203 - 262
8X-RAY DIFFRACTION8( CHAIN A AND RESID 263:301 )A263 - 301

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