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- PDB-4jyk: Structure of E. coli Transcriptional Regulator RutR with bound uracil -

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Basic information

Entry
Database: PDB / ID: 4jyk
TitleStructure of E. coli Transcriptional Regulator RutR with bound uracil
ComponentsHTH-type transcriptional regulator RutR
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Helix-turn-Helix / Transcriptional Regulator
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
Transcription regulator YcdC, C-terminal / Transcription regulator, pyrimidine utilisation, RutR / YcdC-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like ...Transcription regulator YcdC, C-terminal / Transcription regulator, pyrimidine utilisation, RutR / YcdC-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URACIL / HTH-type transcriptional regulator RutR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.7 Å
AuthorsCooper, D.R. / Knapik, A.A. / Petkowski, J.J. / Porebski, P.J. / Osinski, T. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Structure of E. coli Transcriptional Regulator RutR with bound uracil
Authors: Cooper, D.R. / Knapik, A.A. / Petkowski, J.J. / Porebski, P.J. / Osinski, T. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 regulator RutR
B: HTH-type transcriptional regulator RutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,33011
Polymers47,4332
Non-polymers8979
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-126 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.150, 86.140, 69.019
Angle α, β, γ (deg.)90.00, 106.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 17 - 211 / Label seq-ID: 17 - 211

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein HTH-type transcriptional regulator RutR / Rut operon repressor


Mass: 23716.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1013, JW0998, rutR, ycdC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0ACU2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 200 mM Lithium Sulfate, 0.1 M Bis-TRIS pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2012
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Number: 268758 / Rmerge(I) obs: 0.062 / Χ2: 1.38 / D res high: 1.5 Å / D res low: 40 Å / Num. obs: 71325 / % possible obs: 91.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.074099.710.0352.14
3.234.0710010.042.5614.1
2.823.2310010.0552.5444.1
2.562.8210010.062.0574.2
2.382.5699.910.0691.8034.2
2.242.3810010.0821.754.2
2.132.2410010.1011.4514.2
2.042.1310010.1211.2114.2
1.962.0410010.161.0194.2
1.891.9610010.2220.9134.2
1.831.8910010.2970.8514.2
1.781.8310010.4060.8144.2
1.731.7810010.5140.7984.2
1.691.7310010.6630.7593.7
1.651.6910010.7770.7423.3
1.621.6590.510.9090.7382.8
1.581.627810.9450.7152.4
1.551.586710.6652
1.531.5552.710.6431.7
1.51.5336.910.5991.5
ReflectionResolution: 1.5→40 Å / Num. obs: 71325 / % possible obs: 91.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.69
Reflection shellResolution: 1.5→1.53 Å / % possible all: 36.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 1.7→36.75 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.213 / SU ML: 0.05 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16961 2706 5.1 %RANDOM
Rwork0.11962 ---
obs0.12213 50593 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-0.43 Å2
2--0.2 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 51 279 3431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193296
X-RAY DIFFRACTIONr_bond_other_d0.0060.023226
X-RAY DIFFRACTIONr_angle_refined_deg1.751.9864485
X-RAY DIFFRACTIONr_angle_other_deg1.27837410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8815415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05923.383133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67715572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0361521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213653
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02748
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.25433293
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded28.48953222
Refine LS restraints NCS

Ens-ID: 1 / Number: 11610 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 189 -
Rwork0.169 3740 -
obs--100 %

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