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- PDB-7aco: Crystal structure of E. coli HTH-type transcriptional regulator R... -

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Basic information

Entry
Database: PDB / ID: 7aco
TitleCrystal structure of E. coli HTH-type transcriptional regulator RcdA in complex with Tris at 1.80 A resolution
ComponentsHTH-type transcriptional regulator RcdA
KeywordsGENE REGULATION / transcription factor / HTH motif / DNA-binding protein
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal, group 31 / Tetracyclin repressor-like, C-terminal domain / 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
HTH-type transcriptional regulator RcdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsPietrzyk-Brzezinska, A.J. / Cociurovscaia, A.
CitationJournal: Proteins / Year: 2022
Title: Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands.
Authors: Pietrzyk-Brzezinska, A.J. / Cociurovscaia, A.
History
DepositionSep 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator RcdA
B: HTH-type transcriptional regulator RcdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3084
Polymers41,0632
Non-polymers2442
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-10 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.894, 74.688, 51.896
Angle α, β, γ (deg.)90.000, 95.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HTH-type transcriptional regulator RcdA / Regulator of csgD


Mass: 20531.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first two amino acid residues are the remainings of the tag, so they should be numbered (-1) and (0).
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rcdA, ybjK, b0846, JW5114 / Production host: Escherichia coli (E. coli) / References: UniProt: P75811
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M TMAO, 0.1 M Tris pH 8.5, 20% mmePEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.798→39.739 Å / Num. obs: 27595 / % possible obs: 97.7 % / Redundancy: 6.893 % / Biso Wilson estimate: 26.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.11 / Χ2: 0.772 / Net I/σ(I): 12.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.916.8261.4641.2828743455242110.5161.58292.5
1.91-2.046.9770.8062.4828935422741470.790.86998.1
2.04-2.26.8490.4174.7527259400739800.9250.45199.3
2.2-2.416.7810.2617.3524200364935690.9640.28297.8
2.41-2.697.1560.1611.7923735332433170.9890.17399.8
2.69-3.116.8950.09617.9220217294829320.9960.10499.5
3.11-3.86.760.05328.9816372247424220.9980.05897.9
3.8-5.366.980.0439.7313527194519380.9990.04399.6
5.36-39.7396.690.0441.247219111010790.9990.04397.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5I

5x5i


Resolution: 1.798→39.739 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 1380 5 %
Rwork0.1546 26214 -
obs0.1571 27594 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.41 Å2 / Biso mean: 32.8646 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 1.798→39.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 24 320 3162
Biso mean--35.14 40.76 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072998
X-RAY DIFFRACTIONf_angle_d1.0114072
X-RAY DIFFRACTIONf_chiral_restr0.039450
X-RAY DIFFRACTIONf_plane_restr0.005525
X-RAY DIFFRACTIONf_dihedral_angle_d14.4271155
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7982-1.86250.33411270.2748242191
1.8625-1.9370.26891340.2408255195
1.937-2.02520.29211390.2094264198
2.0252-2.13190.2311400.1748264399
2.1319-2.26550.19771370.1618261598
2.2655-2.44040.24621390.1586263599
2.4404-2.68590.23211410.16392685100
2.6859-3.07450.21381410.1629267599
3.0745-3.8730.18151390.1325263598
3.873-39.7390.16041430.1265271399
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)
11.1442-0.12660.50540.9818-0.0421.6781-0.0206-0.01710.01920.37670.0291-0.3593-0.06820.1608-0.00290.28430.0203-0.0530.3081-0.02890.245423.097718.695133.0693
21.1953-0.3948-0.55121.49880.23571.6269-0.0017-0.08980.0022-0.03220.0122-0.09740.15090.1501-0.00740.14240.02250.0020.1642-0.00040.180114.073212.62778.8084
31.1049-0.8753-0.42220.7430.31920.84470.0829-0.07440.0687-0.0037-0.02750.4148-0.093-0.1606-0.06210.27940.02120.03240.2822-0.03630.3831-2.264938.551729.8282
40.7353-0.06820.12991.4170.0641.80370.0666-0.00780.1191-0.2127-0.04280.0219-0.2973-0.1138-0.0090.2280.02750.00610.19030.00170.21164.937226.81526.3319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:64)A6 - 64
2X-RAY DIFFRACTION2(chain A and resid 65:178)A65 - 178
3X-RAY DIFFRACTION3(chain B and resid -1:47)B-1 - 47
4X-RAY DIFFRACTION4(chain B and resid 48:178)B48 - 178

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