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

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Basic information

Entry
Database: PDB / ID: 7acm
TitleCrystal structure of E. coli HTH-type transcriptional regulator RcdA in complex with TMAO at 1.76 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
trimethylamine oxide / HTH-type transcriptional regulator RcdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.763 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)40,8094
Polymers40,6592
Non-polymers1502
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-21 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.762, 74.134, 51.710
Angle α, β, γ (deg.)90.000, 95.190, 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: 20329.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rcdA, ybjK, b0846, JW5114 / Production host: Escherichia coli (E. coli) / References: UniProt: P75811
#2: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 1.84 Å3/Da / Density % sol: 33.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M TMAO, 0.1 M HEPES pH 7.5, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.76→42.294 Å / Num. obs: 28947 / % possible obs: 97.9 % / Redundancy: 6.557 % / Biso Wilson estimate: 24.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Χ2: 1.066 / Net I/σ(I): 14.73 / Num. measured all: 189816
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
1.76-1.876.4320.6082.4228682476044590.8420.6693.7
1.87-26.5010.3794.0828734446944200.9320.41298.9
2-2.166.580.2027.7827115416141210.9780.21999
2.16-2.366.6950.13611.7325427383237980.990.14899.1
2.36-2.646.5090.09816.222189347134090.9940.10698.2
2.64-3.056.750.07122.6920520306930400.9970.07799.1
3.05-3.736.5140.05231.0116689261625620.9980.05797.9
3.73-5.256.4770.04636.9212909202719930.9980.0598.3
5.25-42.2946.60.04238.267550115111440.9980.04599.4

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Processing

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

5x5i


Resolution: 1.763→42.294 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 1448 5 %
Rwork0.1576 27499 -
obs0.1599 28947 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.18 Å2 / Biso mean: 34.7001 Å2 / Biso min: 12.83 Å2
Refinement stepCycle: final / Resolution: 1.763→42.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 15 283 3103
Biso mean--28.99 40.64 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072943
X-RAY DIFFRACTIONf_angle_d1.0363996
X-RAY DIFFRACTIONf_chiral_restr0.038444
X-RAY DIFFRACTIONf_plane_restr0.005514
X-RAY DIFFRACTIONf_dihedral_angle_d14.3221120
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.763-1.82550.29481330.2359252990
1.8255-1.89860.30681460.223277399
1.8986-1.9850.26391460.2056277299
1.985-2.08970.25891450.1848275099
2.0897-2.22060.21241460.1672278099
2.2206-2.3920.22011460.1679276099
2.392-2.63270.20881440.1663274898
2.6327-3.01360.23181470.1683279599
3.0136-3.79640.20531460.1397276098
3.7964-42.2940.13791490.1291283299
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)
17.82120.49233.0372.2379-1.13924.31060.0424-0.2120.10040.48550.0067-0.3312-0.04880.0734-0.0770.27490.0388-0.04850.2426-0.04390.18222.67919.020732.8413
22.6721-0.4329-0.08872.70530.93193.0875-0.0475-0.0736-0.0421-0.03980.0081-0.08920.16220.19850.02270.12270.03070.01390.12420.02420.148513.794912.61738.8042
35.7832-1.366-1.14890.34830.3112.1898-0.089-0.1470.39360.20860.03450.8995-0.2427-0.23520.05640.33330.04080.0530.2615-0.06070.53-1.860138.771929.4291
41.45490.02830.03082.10250.1753.66010.0074-0.01850.136-0.211-0.07840.0752-0.4149-0.0920.04160.17480.0307-0.02390.1366-0.00060.175.052326.77866.3351
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)B1 - 47
4X-RAY DIFFRACTION4(chain B and resid 48:178)B48 - 178

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