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- PDB-9t6t: Crystal Structure of the Listeria monocytogenes CadC in complex w... -

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Basic information

Entry
Database: PDB / ID: 9t6t
TitleCrystal Structure of the Listeria monocytogenes CadC in complex with DNA
Components
  • DNA (5'-D(*AP*TP*TP*CP*AP*AP*AP*CP*AP*AP*AP*CP*AP*CP*TP*TP*GP*AP*AP*T)-3')
  • DNA (5'-D(*AP*TP*TP*CP*AP*AP*GP*TP*GP*TP*TP*TP*GP*TP*TP*TP*GP*AP*AP*T)-3')
  • Lmo1102 protein
KeywordsDNA BINDING PROTEIN / CadC-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / : / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
CHROMIUM ION / DNA / DNA (> 10) / Lmo1102 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsLisboa, J. / Morais-Cabral, J.H. / Cabanes, D.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)UIDB/04293/2020 Portugal
CitationJournal: To Be Published
Title: Crystal Structure of the Listeria monocytogenes CadC in complex with DNA
Authors: Lisboa, J. / Morais-Cabral, J.H. / Cabanes, D.
History
DepositionNov 7, 2025Deposition site: PDBE / Processing site: PDBE
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: Lmo1102 protein
C: DNA (5'-D(*AP*TP*TP*CP*AP*AP*AP*CP*AP*AP*AP*CP*AP*CP*TP*TP*GP*AP*AP*T)-3')
B: Lmo1102 protein
D: DNA (5'-D(*AP*TP*TP*CP*AP*AP*GP*TP*GP*TP*TP*TP*GP*TP*TP*TP*GP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3488
Polymers35,1404
Non-polymers2084
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-86 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.503, 82.073, 38.476
Angle α, β, γ (deg.)90.000, 98.306, 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 Lmo1102 protein


Mass: 11438.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo1102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y817
#2: DNA chain DNA (5'-D(*AP*TP*TP*CP*AP*AP*AP*CP*AP*AP*AP*CP*AP*CP*TP*TP*GP*AP*AP*T)-3')


Mass: 6094.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes EGD-e (bacteria)
#3: DNA chain DNA (5'-D(*AP*TP*TP*CP*AP*AP*GP*TP*GP*TP*TP*TP*GP*TP*TP*TP*GP*AP*AP*T)-3')


Mass: 6169.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Listeria monocytogenes EGD-e (bacteria)
#4: Chemical
ChemComp-CR / CHROMIUM ION


Mass: 51.996 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cr
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.1 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005M Sodium chromate tetrahydrate, 0.005M Sodium molybdate dihydrate, 0.005M Sodium tungstate dihydrate, 0.005M Sodium orthovanadate, 0.1M BES pH 7.5, 0.1M Triethanolamine (TEA) pH 7.5, ...Details: 0.005M Sodium chromate tetrahydrate, 0.005M Sodium molybdate dihydrate, 0.005M Sodium tungstate dihydrate, 0.005M Sodium orthovanadate, 0.1M BES pH 7.5, 0.1M Triethanolamine (TEA) pH 7.5, 15% w/v PEG 3000, 20% v/v 1, 2, 4-Butanetriol, 1% w/v NDSB 256

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.69→42.7 Å / Num. obs: 33727 / % possible obs: 97.47 % / Redundancy: 2.4 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05328 / Rpim(I) all: 0.04227 / Rrim(I) all: 0.06837 / Net I/σ(I): 4.82
Reflection shellResolution: 1.69→1.74 Å / Rmerge(I) obs: 1.648 / Mean I/σ(I) obs: 0.48 / Num. unique obs: 5522 / CC1/2: 0.408 / Rpim(I) all: 1.309 / Rrim(I) all: 2.115

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→42.68 Å / SU ML: 0.2997 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 48.8526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The data were initially consistent with a higher-symmetry space group (C21); however, refinement in this setting imposed constraints that prevented independent modelling of the complementary ...Details: The data were initially consistent with a higher-symmetry space group (C21); however, refinement in this setting imposed constraints that prevented independent modelling of the complementary DNA strands. Analysis of the model and electron density maps indicated that the strands are not related by strict symmetry. Refinement in the lower-symmetry space group P21 allowed independent modelling and resulted in improved interpretability of the electron density, despite higher Rwork and Rfree values.
RfactorNum. reflection% reflection
Rfree0.2854 1641 4.87 %
Rwork0.2478 32081 -
obs0.2496 33722 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.37 Å2
Refinement stepCycle: LAST / Resolution: 1.69→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 814 4 145 2561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072542
X-RAY DIFFRACTIONf_angle_d0.86453604
X-RAY DIFFRACTIONf_chiral_restr0.0454446
X-RAY DIFFRACTIONf_plane_restr0.0051302
X-RAY DIFFRACTIONf_dihedral_angle_d23.17231074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.53381620.52132639X-RAY DIFFRACTION95.7
1.74-1.80.41941500.43012639X-RAY DIFFRACTION98.8
1.8-1.860.39871140.38792732X-RAY DIFFRACTION98.85
1.86-1.940.40781390.37122703X-RAY DIFFRACTION98.68
1.94-2.030.35811290.33412708X-RAY DIFFRACTION98.71
2.03-2.130.32591430.27292674X-RAY DIFFRACTION98.26
2.13-2.270.31251170.2672508X-RAY DIFFRACTION90.92
2.27-2.440.32641350.25272640X-RAY DIFFRACTION96.96
2.44-2.690.31281470.25422722X-RAY DIFFRACTION99.45
2.69-3.080.27711160.24522750X-RAY DIFFRACTION99.58
3.08-3.870.28511430.20342689X-RAY DIFFRACTION97.29
3.87-42.680.19871460.19082677X-RAY DIFFRACTION96.32
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)
11.04226043997-0.150715043049-0.1218792792520.594776621551-0.6873020347610.7375070531530.140723895298-0.522123825716-0.285329028787-0.0856805168772-0.0166557360154-0.07315394005230.145775698835-0.09042898010090.0003267174049550.1831569995510.002462930263930.04589022765940.2667800283560.03303560048540.407757752332-0.7387785856983.78744787138-1.24805587249
21.7613705153-0.1314749453461.026640041620.8158273862020.3342836177161.383244846770.0506858635605-0.00565942862368-0.2185981896630.3124113691940.0560790633286-0.258300321305-0.0225553545075-0.01290197500774.47495458288E-50.317173578375-0.02758496847950.03867996785180.3015924843040.03242287587980.29763672085522.15593822396.2090005716612.572915323
30.7439019615590.0451118180548-0.275859202080.606929866558-0.1867949092040.123044509315-0.2721889658150.04337956064130.004358164697920.5603542949220.3020006190130.168883128361-0.555168379957-0.262111912814-0.0003204922466880.4892694957820.0848693209244-0.07749525308910.298890134582-0.003031749660930.3663384081921.02123641225.75026953513.2729037822
40.515837829664-0.160450615197-0.3809897249261.439975016570.2884209915430.4963517127750.0655768100219-0.10345793454-0.0563230474437-0.3976372829340.2090971494390.141507357737-0.5001955929010.06738050545260.0001403518775450.5675107788020.00953814574886-0.02443030969440.3411034864580.02164129831920.368550303822.9822329449825.2779641433-13.3858549385
51.14289512057-0.2173454242850.9883012063540.743473568491-0.07121670224520.595071170857-0.00557734436881-0.0673305932045-0.249003136502-0.07244005607010.13826827103-0.02590600943240.0298663949916-0.04522765894110.0001038549691940.372406266791-0.000702726462864-0.03517580035130.354080795338-0.007646213921650.31782090165616.73916104323.75364952902-2.98829046192
61.05977530791-0.02535481595980.9770735603520.562684099107-0.1784330649421.15795232816-0.1032945522850.250246832551-0.147245178029-0.0493540806521-0.04198620668860.07376251089120.1932651931920.03105342409897.01135389418E-60.2976002034570.00983350498929-0.01189169050340.2962065570250.02341062278780.3392626451813.775455999037.00689656986-13.2998407871
70.2006122703760.174316513683-0.1065553145230.6557883160440.3240631789640.315844075508-0.2455482448010.0577414792196-0.0552331144347-0.6786541978150.3664681057940.00232003382482-0.56354929970.2785410603560.003978742304050.4564806451630.0181894624212-0.04067343146680.422285199432-0.03009371498530.3551961450374.2506344533225.8172094837-13.2024597406
80.6737371035820.203527293184-0.4603043199241.30175529908-0.3973965551660.5568338359690.1444431637330.107147358148-0.01652915758370.5470895717310.249133854532-0.436091573613-0.1750203798650.168814101070.008677252522270.5546346140350.00539770342539-0.01762392139160.4403865732170.04736105694970.41643674629322.229951131425.279687045113.3286825128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 39 )AA11 - 391 - 29
22chain 'A' and (resid 40 through 112 )AA40 - 11230 - 102
33chain 'C' and (resid 1 through 10 )CB1 - 10
44chain 'C' and (resid 11 through 20 )CB11 - 20
55chain 'B' and (resid 11 through 56 )BC11 - 561 - 46
66chain 'B' and (resid 57 through 112 )BC57 - 11247 - 102
77chain 'D' and (resid 1 through 10 )DD1 - 10
88chain 'D' and (resid 11 through 20 )DD11 - 20

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