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- PDB-6jbx: Crystal structure of Streptococcus pneumoniae FabT in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6jbx
TitleCrystal structure of Streptococcus pneumoniae FabT in complex with DNA
Components
  • DNA (5'-D(*AP*AP*TP*AP*GP*TP*TP*TP*GP*AP*CP*TP*GP*TP*CP*AP*AP*AP*TP*TP*AP*TP*G)-3')
  • DNA (5'-D(*CP*AP*TP*AP*AP*TP*TP*TP*GP*AP*CP*AP*GP*TP*CP*AP*AP*AP*CP*TP*AP*TP*T)-3')
  • Fatty acid biosynthesis transcriptional regulator
KeywordsTRANSCRIPTION/DNA / transcription factor / MarR family / fatty acid synthesis / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
MarR family / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
TRIDECANE / DNA / DNA (> 10) / MarR family transcriptional regulator / HTH marR-type domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZuo, G. / Chen, Z.P. / Li, Q. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570728 China
CitationJournal: Febs Lett. / Year: 2019
Title: Structural insights into repression of the Pneumococcal fatty acid synthesis pathway by repressor FabT and co-repressor acyl-ACP.
Authors: Zuo, G. / Chen, Z.P. / Jiang, Y.L. / Zhu, Z. / Ding, C. / Zhang, Z. / Chen, Y. / Zhou, C.Z. / Li, Q.
History
DepositionJan 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid biosynthesis transcriptional regulator
B: Fatty acid biosynthesis transcriptional regulator
C: DNA (5'-D(*AP*AP*TP*AP*GP*TP*TP*TP*GP*AP*CP*TP*GP*TP*CP*AP*AP*AP*TP*TP*AP*TP*G)-3')
D: DNA (5'-D(*CP*AP*TP*AP*AP*TP*TP*TP*GP*AP*CP*AP*GP*TP*CP*AP*AP*AP*CP*TP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0486
Polymers49,6794
Non-polymers3692
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-88 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.022, 60.868, 74.086
Angle α, β, γ (deg.)90.00, 105.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty acid biosynthesis transcriptional regulator / FabT / MarR family transcriptional regulator / Multiple antibiotic resistance protein MarR / ...FabT / MarR family transcriptional regulator / Multiple antibiotic resistance protein MarR / Transcription regulator / MarR family / Transcriptional regulator


Mass: 17781.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: marR_1, fabT, marR / Plasmid: pET-28a-derived / Production host: Escherichia coli (E. coli) / References: UniProt: A0A062WM61, UniProt: Q8DR18*PLUS
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*GP*TP*TP*TP*GP*AP*CP*TP*GP*TP*CP*AP*AP*AP*TP*TP*AP*TP*G)-3')


Mass: 7093.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae (bacteria)
#3: DNA chain DNA (5'-D(*CP*AP*TP*AP*AP*TP*TP*TP*GP*AP*CP*AP*GP*TP*CP*AP*AP*AP*CP*TP*AP*TP*T)-3')


Mass: 7022.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae (bacteria)
#4: Chemical ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H28
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 0.2 M Sodium acetate trihydrate, 5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 31594 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / CC1/2: 0.857 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Rmerge(I) obs: 0.54 / Num. unique obs: 3169 / CC1/2: 0.857 / Rsym value: 0.54 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→35.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.176 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 1503 4.8 %RANDOM
Rwork0.18763 ---
obs0.18922 30078 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.87 Å2
2---0.25 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 935 26 209 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0143476
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182818
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.5494864
X-RAY DIFFRACTIONr_angle_other_deg0.8421.9576629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1735289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32417.73297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6641522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02619
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4073.8531159
X-RAY DIFFRACTIONr_mcbond_other3.4053.8531160
X-RAY DIFFRACTIONr_mcangle_it4.4165.7521447
X-RAY DIFFRACTIONr_mcangle_other4.4165.7531448
X-RAY DIFFRACTIONr_scbond_it5.2444.7912317
X-RAY DIFFRACTIONr_scbond_other5.2434.7912317
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4767.0383418
X-RAY DIFFRACTIONr_long_range_B_refined8.50747.2974218
X-RAY DIFFRACTIONr_long_range_B_other8.47546.9984166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 107 -
Rwork0.236 2175 -
obs--96.33 %

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