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- PDB-6z1b: Structure of K52-acetylated RutR in complex with uracil. -

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Basic information

Entry
Database: PDB / ID: 6z1b
TitleStructure of K52-acetylated RutR in complex with uracil.
ComponentsHTH-type transcriptional regulator RutR
KeywordsTRANSCRIPTION / transcriptional repressor / Escherichia coli / lysine-acetylation / RutR / TetR-class
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 / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
URACIL / HTH-type transcriptional regulator RutR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsKremer, M. / Schulze, S. / Lammers, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA 2984/5 Germany
CitationJournal: To Be Published
Title: Structure of K52-acetylated RutR in complex with uracil.
Authors: Kremer, M. / Schulze, S. / Baumann, U.
History
DepositionMay 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_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
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)49,9607
Polymers49,5502
Non-polymers4105
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-29 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.307, 88.547, 150.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 13 through 70 or resid 72 through 213))
21(chain B and (resid 13 through 70 or resid 72 through 213))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain A and (resid 13 through 70 or resid 72 through 213))AA13 - 7015 - 72
12GLNGLNHISHIS(chain A and (resid 13 through 70 or resid 72 through 213))AA72 - 21374 - 215
21SERSERLEULEU(chain B and (resid 13 through 70 or resid 72 through 213))BB13 - 7015 - 72
22GLNGLNHISHIS(chain B and (resid 13 through 70 or resid 72 through 213))BB72 - 21374 - 215

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Components

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


Mass: 24774.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The structure contains acetyl-L-lysine at position K52.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rutR, ycdC, b1013, JW0998 / Plasmid: pRSF-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ACU2
#2: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 % precipitation mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol), 0.1 M buffer system 4 (MOPSO, Bis-Tris pH 6.5), 100 mM amino acids mix 2 (0.2M DL-Arginine hydrochloride, 0.2M DL- ...Details: 50 % precipitation mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-Hexanetriol), 0.1 M buffer system 4 (MOPSO, Bis-Tris pH 6.5), 100 mM amino acids mix 2 (0.2M DL-Arginine hydrochloride, 0.2M DL-Threonine, 0.2M DL-Histidine monohydrochloride monohydrate, 0.2M DL-5- Hydroxylysine hydrochloride, 0.2M trans-4-hydroxy-L-proline)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2018 / Details: Microdiffractometer MD3Up
RadiationCollimation: Vertical CRL/horizontal elliptical mirror / Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.31 Å / Num. obs: 31447 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.046 / Rrim(I) all: 0.116 / Net I/σ(I): 9.8 / Num. measured all: 199389 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.326.41.3251815528590.5210.5711.4451.5100
9-48.3150.05528935830.9960.0270.06224.999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.54 Å45.98 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSJun 1, 2017data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JYK

1jyk


Resolution: 2.25→45.98 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1570 5.01 %
Rwork0.1931 29798 -
obs0.1942 31368 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.74 Å2 / Biso mean: 61.3075 Å2 / Biso min: 32.59 Å2
Refinement stepCycle: final / Resolution: 2.25→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 30 216 3449
Biso mean--97.58 59.56 -
Num. residues----405
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1210X-RAY DIFFRACTION7.435TORSIONAL
12B1210X-RAY DIFFRACTION7.435TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.320.33271460.305826642810
2.32-2.410.31261390.262826682807
2.41-2.50.32021290.25726672796
2.5-2.620.29661400.231826682808
2.62-2.750.27011480.228326602808
2.75-2.930.21661340.208927002834
2.93-3.150.27231250.219427172842
3.15-3.470.23661450.198927182863
3.47-3.970.19561720.180426832855
3.97-50.17351530.149927502903
5-45.980.17541390.176829033042
Refinement TLS params.Method: refined / Origin x: -7.5495 Å / Origin y: 19.3922 Å / Origin z: -27.4843 Å
111213212223313233
T0.3794 Å2-0.0224 Å20.023 Å2-0.4602 Å20.0054 Å2--0.4207 Å2
L1.4616 °2-0.2874 °21.1108 °2-1.167 °2-0.1444 °2--1.7157 °2
S0.0181 Å °0.2554 Å °0.089 Å °0.0069 Å °-0.0824 Å °-0.0478 Å °-0.0731 Å °0.294 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 213
2X-RAY DIFFRACTION1allB12 - 213
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 3
5X-RAY DIFFRACTION1allE1 - 251

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