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- PDB-4u0w: Crystal structure of YvoA from Bacillus subtilis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4u0w
TitleCrystal structure of YvoA from Bacillus subtilis in complex with N-acetylglucosamine-6-phosphate
ComponentsHTH-type transcriptional repressor YvoA
KeywordsTRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Chorismate lyase fold / N-acetylglucosamine utilization
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
Chem-16G / HTH-type transcriptional repressor NagR
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_audit_support / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_site / 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 / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,24119
Polymers55,6472
Non-polymers1,59317
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint25 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.142, 99.142, 353.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yvoA, BSU35030 / Production host: Escherichia coli (E. coli) / References: UniProt: O34817
#2: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Na-HEPES salt, 200 mM ammonium chloride, 25 % (v/v) glycerol ethoxylate

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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: Dec 17, 2011
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→32.73 Å / Num. obs: 45784 / % possible obs: 99.9 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.15
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 2.39 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2wv0

2wv0


Resolution: 2.001→32.727 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 2291 5.01 %Random selection
Rwork0.2052 43451 --
obs0.2077 45742 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 41.2875 Å2 / Biso min: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 2.001→32.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 102 253 4199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084061
X-RAY DIFFRACTIONf_angle_d1.0875470
X-RAY DIFFRACTIONf_chiral_restr0.043604
X-RAY DIFFRACTIONf_plane_restr0.006707
X-RAY DIFFRACTIONf_dihedral_angle_d14.8381565
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0007-2.04420.38761430.32382702284599
2.0442-2.09170.36381410.281126612802100
2.0917-2.1440.3431390.285826522791100
2.144-2.2020.2971440.258727092853100
2.202-2.26680.29751410.253526622803100
2.2668-2.33990.31971420.246626932835100
2.3399-2.42350.27861410.239726862827100
2.4235-2.52050.27981420.228527062848100
2.5205-2.63520.28861410.226226862827100
2.6352-2.77410.29451430.236227232866100
2.7741-2.94780.321420.227726932835100
2.9478-3.17520.27471440.217527292873100
3.1752-3.49440.24891450.199927482893100
3.4944-3.99930.20211440.181127392883100
3.9993-5.03570.20211460.155327762922100
5.0357-32.73120.22441530.18328863039100

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