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- PDB-4x1e: Crystal structure of unliganded E. coli transcriptional regulator... -

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Basic information

Entry
Database: PDB / ID: 4x1e
TitleCrystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant
ComponentsHTH-type transcriptional regulator RutR
KeywordsTRANSCRIPTION / transcriptional regulator / TetR family member / arginine and pyrimidine biosynthesis / DNA binding
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
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
HTH-type transcriptional regulator RutR
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsNguyen Le Minh, P. / de Cima, S. / Bervoets, I. / Maes, D. / Rubio, V. / Charlier, D.
Funding support Belgium, Spain, 6items
OrganizationGrant numberCountry
Research Foundation Flanders (FWO-Vlaanderen)G.0429.06 Belgium
Research Council of the Vrije Universiteit Brussel (OZR-VUB) Belgium
Vlaamse Gemeenschapscommissie Belgium
Spanish GovernmentBFU2011-30407 Spain
Valencian GovernmentPrometeo II/2014/029 Spain
Instituto de Salud Carlos III-CIBERER Spain
CitationJournal: Febs Open Bio / Year: 2015
Title: Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli.
Authors: Nguyen Le Minh, P. / de Cima, S. / Bervoets, I. / Maes, D. / Rubio, V. / Charlier, D.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)49,2012
Polymers49,2012
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-40 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.420, 91.770, 97.710
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
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 21 - 211 / Label seq-ID: 21 - 211

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is the same as asym.

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Components

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


Mass: 24600.557 Da / Num. of mol.: 2 / Mutation: W167A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: rutR, c1150 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ACU3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % (w/v) methanol, 10 mM CaCl2 and 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→66.893 Å / Num. all: 17045 / Num. obs: 17045 / % possible obs: 97.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.8 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.101 / Rsym value: 0.087 / Net I/av σ(I): 6.333 / Net I/σ(I): 7.9 / Num. measured all: 61883
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.533.60.3322.1884824850.1890.3323.198.6
2.53-2.683.70.2762.5879923600.1520.276498.6
2.68-2.873.60.2083.2788521690.1170.2085.196
2.87-3.13.60.1524.2728020320.0850.1526.697.8
3.1-3.393.70.1076714419080.0570.1078.898.2
3.39-3.793.60.0837.7613716940.0460.08310.795.9
3.79-4.383.60.0639.6561115390.0350.06312.797.6
4.38-5.373.70.05810.5474312860.0320.05813.696.1
5.37-7.593.60.05511.3361210170.0310.05512.696.2
7.59-19.6983.30.04211.518245550.0240.04214.189.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.7 Å
Translation2.5 Å19.7 Å

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Processing

Software
NameVersionClassification
MOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.3.0phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LOC

3loc


Resolution: 2.4→66.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2501 / WRfactor Rwork: 0.2002 / FOM work R set: 0.7703 / SU B: 21.792 / SU ML: 0.242 / SU R Cruickshank DPI: 0.4655 / SU Rfree: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.465 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 865 5.1 %RANDOM
Rwork0.1945 16147 --
obs0.1972 16147 96.33 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 264.55 Å2 / Biso mean: 58.072 Å2 / Biso min: 28.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--1.19 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 2.4→66.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 0 91 3177
Biso mean---48.56 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193160
X-RAY DIFFRACTIONr_bond_other_d0.0040.023132
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9784283
X-RAY DIFFRACTIONr_angle_other_deg1.0337192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9935391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56823.676136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34815555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.861521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213526
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02711
X-RAY DIFFRACTIONr_mcbond_it1.7911.351567
X-RAY DIFFRACTIONr_mcbond_other1.7881.3471566
X-RAY DIFFRACTIONr_mcangle_it2.7722.0151957
Refine LS restraints NCS

Ens-ID: 1 / Number: 11039 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 71 -
Rwork0.231 1184 -
all-1255 -
obs--97.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.72620.3816-2.69454.99630.97136.08050.11480.46590.78-0.0364-0.0310.3056-0.2987-0.5711-0.08380.17780.01630.00310.06150.03210.57234.35527.417-20.472
24.45133.6798-3.357910.7529-6.07377.57070.2315-0.5149-0.186-0.2463-0.1928-0.61450.03030.5708-0.03870.0779-0.0272-0.01820.2326-0.05850.6615-0.9213.158-5.551
33.26451.94850.97554.48780.477812.6427-0.00340.43350.1516-0.4470.2215-0.1308-0.55470.8974-0.21810.0911-0.05720.02670.2586-0.03880.6848-5.10213.763-16.04
49.48562.8235-4.05318.3844-4.606910.4922-0.09010.0195-0.3823-0.3591-0.1923-0.6030.2490.54040.28240.09810.0472-0.05970.05-0.04990.6253-4.177-6.708-11.495
52.421-0.4768-0.19185.6180.40973.8006-0.033-0.34830.10820.16970.06170.0361-0.1517-0.1491-0.02870.0150.0002-0.00890.13-0.05270.609-15.6719.139-3.072
620.7172-3.048621.373632.6416-26.276939.7551.87911.73771.2477-6.4602-4.0339-2.70756.37814.26552.15481.97430.98540.83150.73790.53791.3462-23.38318.93-35.972
73.25690.7802-5.64551.284-2.110910.3262-0.71870.5417-0.3504-0.69230.86080.89161.4977-1.4467-0.1422.86230.7756-0.06821.45120.46291.2847-29.38423.029-43.223
81.61891.56621.271837.377-15.596924.17270.47270.54930.0819-0.2022-0.4022-0.7751-0.4969-0.1689-0.07050.24960.25280.05150.29410.02410.6653-29.06220.377-27.947
93.9651.4844-6.70055.4584-4.246815.6444-0.02330.1230.2233-0.0655-0.05330.5226-0.4077-0.7640.07660.09080.0139-0.09570.2590.09880.9132-33.231.542-9.716
102.1761-0.60440.16833.6126-0.66682.31660.1376-0.1009-0.0987-0.2956-0.10270.2681-0.0933-0.0165-0.03490.0452-0.001-0.07880.0447-0.01670.6443-21.9855.107-13.728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 70
2X-RAY DIFFRACTION2A71 - 98
3X-RAY DIFFRACTION3A99 - 129
4X-RAY DIFFRACTION4A130 - 160
5X-RAY DIFFRACTION5A161 - 211
6X-RAY DIFFRACTION6B15 - 43
7X-RAY DIFFRACTION7B44 - 56
8X-RAY DIFFRACTION8B57 - 76
9X-RAY DIFFRACTION9B77 - 96
10X-RAY DIFFRACTION10B97 - 211

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