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- PDB-7zhe: Crystal structure of CtaZ from Ruminiclostridium cellulolyticum -

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Basic information

Entry
Database: PDB / ID: 7zhe
TitleCrystal structure of CtaZ from Ruminiclostridium cellulolyticum
ComponentsTranscription activator effector binding
KeywordsLIPID BINDING PROTEIN / GYRASE-LIKE DOMAIN / RECEPTOR / SIDEROPHORE / SELF PROTECTION / ANTIBIOTIC RESISTANCE / DRUG BINDING
Function / homology
Function and homology information


Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Transcription activator effector binding
Similarity search - Component
Biological speciesRuminiclostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,6884
Polymers17,5501
Non-polymers1383
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-17 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.340, 121.340, 108.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-202-

NA

21A-334-

HOH

31A-349-

HOH

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Components

#1: Protein Transcription activator effector binding


Mass: 17550.410 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M NaAc

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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: 2→30 Å / Num. obs: 20682 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2807 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZHD

7zhd


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.547 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1034 5 %RANDOM
Rwork0.1807 ---
obs0.1821 19640 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.44 Å2 / Biso mean: 45.487 Å2 / Biso min: 29.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 8 98 1285
Biso mean--64.58 51.99 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131208
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171148
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.6581632
X-RAY DIFFRACTIONr_angle_other_deg1.0871.5682684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30823.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27315211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.828154
X-RAY DIFFRACTIONr_chiral_restr0.0460.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_rigid_bond_restr0.7432354
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 77 -
Rwork0.314 1456 -
all-1533 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: -6.1331 Å / Origin y: -18.1165 Å / Origin z: -38.6975 Å
111213212223313233
T0.0345 Å2-0.0109 Å2-0.0204 Å2-0.0221 Å20.0246 Å2--0.0706 Å2
L0.1051 °20.2912 °2-0.025 °2-1.1715 °20.1745 °2--0.1859 °2
S-0.0069 Å °-0.0046 Å °0.0281 Å °-0.0223 Å °0.0408 Å °0.0502 Å °0.0298 Å °0.0265 Å °-0.0339 Å °

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