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- PDB-4u0y: Crystal structure of the DNA-binding domains of YvoA in complex w... -

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Basic information

Entry
Database: PDB / ID: 4u0y
TitleCrystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA
Components
  • DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-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 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 ...UTRA / UbiC transcription regulator-associated / UTRA domain / : / 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 / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH-type transcriptional repressor NagR
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsFillenberg, 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
DepositionJul 14, 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 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / 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 / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.tip / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional repressor YvoA
B: HTH-type transcriptional repressor YvoA
C: HTH-type transcriptional repressor YvoA
D: HTH-type transcriptional repressor YvoA
E: DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3')
F: DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1028
Polymers45,0316
Non-polymers712
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-68 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.554, 48.554, 153.941
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
HTH-type transcriptional repressor YvoA


Mass: 8965.283 Da / Num. of mol.: 4 / Fragment: UNP residues 1-75
Source method: isolated from a genetically manipulated source
Details: Truncated form of YvoA; comprises only the DNA-binding domain (residues 1-75)
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yvoA, BSU35030 / Production host: Escherichia coli (E. coli) / References: UniProt: O34817
#2: DNA chain DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3')


Mass: 4584.984 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 15mer palindromic dsDNA 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM sodium cacodylate, 200 mM sodium citrate, 10 mM MgCl2, 5 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 8, 2010
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: 1.91→32.52 Å / Num. obs: 31230 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.86 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.61
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA-binding domain of PDB entry 2wv0

2wv0


Resolution: 1.91→32.52 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8245 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1558 5 %Random selection
Rwork0.1783 29632 --
obs0.1809 31190 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.38 Å2 / Biso mean: 29.8537 Å2 / Biso min: 13.23 Å2
Refinement stepCycle: LAST / Resolution: 1.91→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 614 2 287 3323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073176
X-RAY DIFFRACTIONf_angle_d1.0874407
X-RAY DIFFRACTIONf_chiral_restr0.046482
X-RAY DIFFRACTIONf_plane_restr0.005472
X-RAY DIFFRACTIONf_dihedral_angle_d19.6761303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.914-1.97580.31291390.26712660279998
1.9758-2.04640.291430.233827162859100
2.0464-2.12830.25851400.219326742814100
2.1283-2.22520.28771430.205927122855100
2.2252-2.34250.28161410.205526952836100
2.3425-2.48920.23411420.19526842826100
2.4892-2.68130.23871440.197727402884100
2.6813-2.9510.25671400.191626572797100
2.951-3.37760.24881420.169827082850100
3.3776-4.25390.19511410.148226862827100
4.2539-32.52860.17881430.147627002843100

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