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- PDB-7zhd: Crystal structure of CtaZ in complex with Closthioamide -

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Basic information

Entry
Database: PDB / ID: 7zhd
TitleCrystal structure of CtaZ in complex with Closthioamide
ComponentsTranscription activator effector binding
KeywordsLIPID BINDING PROTEIN / GYRASE-LIKE DOMAIN / RECEPTOR / SIDEROPHORE / SELF PROTECTION / ANTIBIOTIC RESISTANCE / DRUG BINDING
Function / homologyBacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / metal ion binding / Chem-IQ4 / Transcription activator effector binding
Function and homology information
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsGude, F. / Molloy, E.M. / Horch, T. / Dell, M. / Dunbar, K.L. / Krabbe, J. / Groll, M. / Hertweck, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme283570European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: A Specialized Polythioamide-Binding Protein Confers Antibiotic Self-Resistance in Anaerobic Bacteria.
Authors: Gude, F. / Molloy, E.M. / Horch, T. / Dell, M. / Dunbar, K.L. / Krabbe, J. / Groll, M. / Hertweck, C.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription activator effector binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4186
Polymers17,4471
Non-polymers9715
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-43 kcal/mol
Surface area8260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.640, 40.850, 44.810
Angle α, β, γ (deg.)90.000, 91.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transcription activator effector binding


Mass: 17447.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium cellulolyticum (bacteria)
Gene: Ccel_3263 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: B8I0Z6

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Non-polymers , 5 types, 70 molecules

#2: Chemical ChemComp-IQ4 / ~{N}-[3-[[3-[3-[3-[3-[(4-hydroxyphenyl)carbothioylamino]propanethioylamino]propanethioylamino]propylamino]-3-sulfanylidene-propyl]amino]-3-sulfanylidene-propyl]-4-oxidanyl-benzenecarbothioamide / Closthioamide


Mass: 695.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H38N6O2S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM Na-cacodylate, 200 mM ZnAc2, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 22520 / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.9
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3648 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.036 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1125 5 %RANDOM
Rwork0.1743 ---
obs0.1755 21391 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.09 Å2 / Biso mean: 35.699 Å2 / Biso min: 22.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å2-0 Å2-1.88 Å2
2---1.89 Å20 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 54 65 1282
Biso mean--45.6 39.4 -
Num. residues----149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131243
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171171
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.6951679
X-RAY DIFFRACTIONr_angle_other_deg1.091.6152737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04223.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70915208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.54154
X-RAY DIFFRACTIONr_chiral_restr0.0440.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_rigid_bond_restr1.02932414
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 84 -
Rwork0.324 1597 -
all-1681 -
obs--99.29 %
Refinement TLS params.Method: refined / Origin x: 33.0722 Å / Origin y: 38.5759 Å / Origin z: 30.2599 Å
111213212223313233
T0.0082 Å2-0.0019 Å20.0083 Å2-0.0305 Å20.0002 Å2--0.0114 Å2
L0.0803 °2-0.085 °2-0.0482 °2-0.1613 °20.0539 °2--0.1128 °2
S0.0045 Å °-0.0078 Å °0.0111 Å °-0.0014 Å °0.0002 Å °-0.0183 Å °0.0078 Å °0.0063 Å °-0.0046 Å °

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