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- PDB-4wwc: Crystal structure of full length YvoA in complex with palindromic... -

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Basic information

Entry
Database: PDB / ID: 4wwc
TitleCrystal structure of full length YvoA in complex with palindromic operator DNA
Components
  • DNA (5'-D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3')
  • HTH-type transcriptional repressor YvoA
KeywordsTRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Winged helix-turn-helix motif / N-acetylglucosamine utilization / DNA-binding / Operator-binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. ...UTRA / UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional repressor NagR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsGrau, F.C. / Fillenberg, S.B. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.
Authors: Fillenberg, S.B. / Grau, F.C. / Seidel, G. / Muller, Y.A.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional repressor YvoA
B: HTH-type transcriptional repressor YvoA
E: DNA (5'-D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3')
F: DNA (5'-D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,77311
Polymers67,3394
Non-polymers4347
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-23 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.979, 79.979, 239.963
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HTH-type transcriptional repressor YvoA


Mass: 27823.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Full length YvoA / Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yvoA, BSU35030 / Production host: Escherichia coli (E. coli) / References: UniProt: O34817
#2: DNA chain DNA (5'-D(P*CP*AP*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*TP*GP*G)-3')


Mass: 5845.785 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 19 mer palindromic construct; derived from the consensus sequence of the two native non-palindromic dre-site sequences upstream of nagAB-yvoA and nagP
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.903→34.28 Å / Num. obs: 18046 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 90.49 Å2 / Rmerge(I) obs: 0.09891 / Net I/σ(I): 16.77
Reflection shellResolution: 2.903→3.007 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.979 / Mean I/σ(I) obs: 0.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA-binding and effector-binding domains of YvoA (2WV0)

2wv0


Resolution: 2.903→34.277 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 1442 8 %Random selection
Rwork0.2296 ---
obs0.2336 18031 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.903→34.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 781 28 2 4333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114497
X-RAY DIFFRACTIONf_angle_d1.4666206
X-RAY DIFFRACTIONf_dihedral_angle_d19.5581772
X-RAY DIFFRACTIONf_chiral_restr0.063690
X-RAY DIFFRACTIONf_plane_restr0.007664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9035-3.00720.41271400.34151614X-RAY DIFFRACTION100
3.0072-3.12750.40421410.31991623X-RAY DIFFRACTION100
3.1275-3.26980.39491400.29931614X-RAY DIFFRACTION100
3.2698-3.4420.28741420.26281627X-RAY DIFFRACTION100
3.442-3.65740.32611420.25131635X-RAY DIFFRACTION100
3.6574-3.93940.34791420.23791624X-RAY DIFFRACTION100
3.9394-4.33520.27911440.23051666X-RAY DIFFRACTION100
4.3352-4.96090.24771470.19751679X-RAY DIFFRACTION100
4.9609-6.2440.2661470.21871692X-RAY DIFFRACTION100
6.244-34.27940.22371570.20471815X-RAY DIFFRACTION100

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