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

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Basic information

Entry
Database: PDB / ID: 7acl
TitleCrystal structure of E. coli HTH-type transcriptional regulator RcdA at 2.05 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
DI(HYDROXYETHYL)ETHER / HTH-type transcriptional regulator RcdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 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

Downloads & links

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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)40,7653
Polymers40,6592
Non-polymers1061
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-18 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.595, 76.608, 105.181
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M magnesium formate, 15% PEG3350

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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: 2.049→43.357 Å / Num. obs: 20613 / % possible obs: 98.9 % / Redundancy: 12.624 % / Biso Wilson estimate: 37.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.093 / Χ2: 1.013 / Net I/σ(I): 18.58
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
2.05-2.1710.8640.9542.1134016329931310.774194.9
2.17-2.3213.3880.6453.9241716311931160.9160.67199.9
2.32-2.5112.6280.4096.2136496290528900.9590.42699.5
2.51-2.7513.4560.21911.2335752266026570.9880.22799.9
2.75-3.0712.7980.13516.7831482246524600.9950.14199.8
3.07-3.5413.3060.07729.8128635216021520.9980.0899.6
3.54-4.3312.6460.0544.9423496186418580.9990.05299.7
4.33-6.0912.5190.04551.7918316147214630.9990.04799.4
6.09-43.35711.6330.03658.34103078958860.9990.03899

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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: 2.049→43.357 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1031 5 %
Rwork0.185 19579 -
obs0.1883 20610 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.97 Å2 / Biso mean: 51.6899 Å2 / Biso min: 19.66 Å2
Refinement stepCycle: final / Resolution: 2.049→43.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 7 139 2916
Biso mean--55.42 49.94 -
Num. residues----347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082881
X-RAY DIFFRACTIONf_angle_d0.983905
X-RAY DIFFRACTIONf_chiral_restr0.04435
X-RAY DIFFRACTIONf_plane_restr0.005504
X-RAY DIFFRACTIONf_dihedral_angle_d16.3271093
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.049-2.15670.32571380.2423261694
2.1567-2.29180.31831450.23312763100
2.2918-2.46870.27091480.22392804100
2.4687-2.71710.29311460.22162774100
2.7171-3.11020.28921480.21732810100
3.1102-3.91810.24161490.17672847100
3.9181-43.3570.2061570.148296599
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)
17.05540.4301-2.45035.47732.48757.19190.04431.17680.2139-0.50590.44250.03560.22360.08-0.4220.4179-0.0571-0.04160.5471-0.02970.3753-26.6619-5.7295-35.1709
26.3679-1.42441.43884.7732-0.82516.98640.21030.8375-0.1141-0.7532-0.25890.08741.2242-0.0840.13830.52760.0147-0.04170.2516-0.01120.3105-19.7231-13.3108-8.8546
31.64410.7828-0.25215.0175-0.85353.0242-0.18450.4623-0.058-0.236-0.3923-1.2667-0.43381.67440.54020.3978-0.0726-0.00060.68850.09380.5702-23.18062.7521-21.2225
48.5881-0.14430.60975.6983-0.22856.3477-0.13340.03260.0313-0.07990.0845-0.26660.0590.12460.00330.2431-0.0083-0.00180.1116-0.01740.1867-17.4511-5.306-4.9559
53.7242.9947-3.61087.4411-2.66588.5208-0.18670.77330.5699-0.04280.75240.33-0.3965-1.1258-0.49890.3589-0.03520.08240.56560.05140.3704-1.27916.0259-34.2796
61.95290.3151-3.071.2885-0.58218.65510.1070.06560.18790.1266-0.114-0.2109-0.51060.12-0.00350.2706-0.0447-0.02840.2024-0.00830.4162-7.461812.9892-11.3907
75.6159-2.606-0.43884.3623-0.10885.96720.09970.1308-0.9417-0.0703-0.25580.49690.8956-0.50690.13270.3115-0.0423-0.01970.2893-0.06130.5673-4.04022.0979-21.3419
85.0042-2.23591.60353.9422-2.15197.95990.1302-0.23070.08210.27-0.02250.0321-0.0469-0.1055-0.15710.2331-0.0815-0.00230.1324-0.01710.2309-13.60895.5858-2.9152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:66)A6 - 66
2X-RAY DIFFRACTION2(chain A and resid 67:101)A67 - 101
3X-RAY DIFFRACTION3(chain A and resid 102:126)A102 - 126
4X-RAY DIFFRACTION4(chain A and resid 127:178)A127 - 178
5X-RAY DIFFRACTION5(chain B and resid 5:53)B5 - 53
6X-RAY DIFFRACTION6(chain B and resid 54:103)B54 - 103
7X-RAY DIFFRACTION7(chain B and resid 104:129)B104 - 129
8X-RAY DIFFRACTION8(chain B and resid 130:178)B130 - 178

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