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- PDB-5x5i: The X-ray crystal structure of a TetR family transcription regula... -

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Basic information

Entry
Database: PDB / ID: 5x5i
TitleThe X-ray crystal structure of a TetR family transcription regulator RcdA involved in the regulation of biofilm formation in Escherichia coli
ComponentsHTH-type transcriptional regulator RcdA
KeywordsTRANSCRIPTION / TetR family transcription regulator / master transcription regulator / dimer / biofilm formation
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 / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator RcdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.554 Å
AuthorsSugino, H. / Usui, M. / Shimada, T. / Nakano, M. / Ogasawara, H. / Ishihama, A. / Hirata, A.
Funding support Japan, 2items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research on Innovative Areas JSPS KAKENHI25118516 Japan
Scientific Research (C)JSPS KAKENHI15K06975 Japan
CitationJournal: FEBS Lett. / Year: 2017
Title: A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation.
Authors: Sugino, H. / Usui, T. / Shimada, T. / Nakano, M. / Ogasawara, H. / Ishihama, A. / Hirata, A.
History
DepositionFeb 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release

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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
C: HTH-type transcriptional regulator RcdA
D: HTH-type transcriptional regulator RcdA
E: HTH-type transcriptional regulator RcdA
F: HTH-type transcriptional regulator RcdA
G: HTH-type transcriptional regulator RcdA
H: HTH-type transcriptional regulator RcdA


Theoretical massNumber of molelcules
Total (without water)176,6628
Polymers176,6628
Non-polymers00
Water18010
1
A: HTH-type transcriptional regulator RcdA
E: HTH-type transcriptional regulator RcdA


Theoretical massNumber of molelcules
Total (without water)44,1652
Polymers44,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-21 kcal/mol
Surface area16430 Å2
MethodPISA
2
B: HTH-type transcriptional regulator RcdA
G: HTH-type transcriptional regulator RcdA


Theoretical massNumber of molelcules
Total (without water)44,1652
Polymers44,1652
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-19 kcal/mol
Surface area16610 Å2
MethodPISA
3
C: HTH-type transcriptional regulator RcdA
F: HTH-type transcriptional regulator RcdA


Theoretical massNumber of molelcules
Total (without water)44,1652
Polymers44,1652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-21 kcal/mol
Surface area16460 Å2
MethodPISA
4
D: HTH-type transcriptional regulator RcdA
H: HTH-type transcriptional regulator RcdA


Theoretical massNumber of molelcules
Total (without water)44,1652
Polymers44,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-21 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.477, 75.967, 110.051
Angle α, β, γ (deg.)90.00, 90.01, 89.95
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22082.688 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rcdA, ybjK, b0846, JW5114 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P75811
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.82 Å3/Da / Density % sol: 32.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4% PEG 400, 0.1M HEPES (pH 7.5), 0.2M L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→50.01 Å / Num. obs: 79510 / % possible obs: 98.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 47
Reflection shellResolution: 2.55→2.59 Å / Rmerge(I) obs: 0.292 / Num. unique all: 7568

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.554→37.983 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 28.29 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 3939 4.96 %RANDOM
Rwork0.198 ---
obs0.2013 79481 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.554→37.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10930 0 0 10 10940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111142
X-RAY DIFFRACTIONf_angle_d1.39315052
X-RAY DIFFRACTIONf_dihedral_angle_d21.8126764
X-RAY DIFFRACTIONf_chiral_restr0.0691694
X-RAY DIFFRACTIONf_plane_restr0.0081916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.554-2.58510.36931360.27722464X-RAY DIFFRACTION89
2.5851-2.61790.41521340.23732658X-RAY DIFFRACTION98
2.6179-2.65230.31071440.22392648X-RAY DIFFRACTION98
2.6523-2.68860.31611380.21172666X-RAY DIFFRACTION99
2.6886-2.7270.32141540.20712804X-RAY DIFFRACTION98
2.727-2.76770.2981420.21472623X-RAY DIFFRACTION98
2.7677-2.81090.32221280.21312708X-RAY DIFFRACTION99
2.8109-2.8570.26851400.21042726X-RAY DIFFRACTION98
2.857-2.90630.26121500.21312762X-RAY DIFFRACTION99
2.9063-2.95910.28011380.22162732X-RAY DIFFRACTION99
2.9591-3.0160.34331380.22942576X-RAY DIFFRACTION98
3.016-3.07750.37631400.23582715X-RAY DIFFRACTION99
3.0775-3.14440.34981500.23762738X-RAY DIFFRACTION99
3.1444-3.21750.28641500.22992692X-RAY DIFFRACTION99
3.2175-3.29790.36181440.22132672X-RAY DIFFRACTION99
3.2979-3.3870.30221340.1962735X-RAY DIFFRACTION99
3.387-3.48660.24771500.19492732X-RAY DIFFRACTION99
3.4866-3.59910.3411400.21232686X-RAY DIFFRACTION99
3.5991-3.72760.30041380.19432737X-RAY DIFFRACTION99
3.7276-3.87670.24561540.19092760X-RAY DIFFRACTION100
3.8767-4.0530.22971320.17772707X-RAY DIFFRACTION99
4.053-4.26640.2281380.16822727X-RAY DIFFRACTION99
4.2664-4.53330.21551240.17662699X-RAY DIFFRACTION99
4.5333-4.88270.21921380.15762770X-RAY DIFFRACTION100
4.8827-5.37280.25271340.18852769X-RAY DIFFRACTION99
5.3728-6.14740.23581260.24092712X-RAY DIFFRACTION100
6.1474-7.73430.24221520.2042789X-RAY DIFFRACTION99
7.7343-37.98770.2031530.16732535X-RAY DIFFRACTION95
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)
11.31940.0893-0.62691.21950.45752.2134-0.03620.2816-0.0865-0.14540.0447-0.0257-0.1593-0.0236-0.03620.2966-0.00880.01240.3283-0.04750.1949-7.389231.6008-36.6102
21.2761-1.2583-2.57671.28520.80233.77490.1564-0.09750.0758-0.2933-0.06880.0199-0.2430.1545-0.10350.2753-0.0352-0.0430.3251-0.06340.2681-2.0807-2.51090.2546
31.0879-0.08120.78891.7047-0.45862.4827-0.02910.35010.0516-0.178-0.0191-0.02250.01730.0405-0.01540.2654-0.01390.01220.36350.01410.17935.983319.639117.6628
41.187-1.11752.84341.2152-1.48793.35120.1568-0.0369-0.1254-0.3003-0.05110.01780.2893-0.0992-0.10460.32990.0050.05420.33770.03070.25951.307453.9061-54.746
50.93991.11932.3360.71961.253.21170.13890.0757-0.10250.2149-0.05890.03430.30910.1115-0.07230.327-0.00260.04170.3527-0.0450.2744-21.785515.8353-34.7804
61.0140.5565-2.04721.0199-0.53433.41960.05180.05070.04090.2045-0.03360.002-0.078-0.087-0.05380.3104-0.0179-0.0220.34880.00870.260220.331335.344520.4102
71.3781-0.00190.6471.84540.87843.0694-0.0353-0.35080.04740.340.06880.04490.29990.039-0.02790.31130.03740.00470.3363-0.03080.140112.0186-18.20973.1969
81.07950.1956-0.65051.7919-0.92142.3653-0.0013-0.3195-0.03560.22590.0449-0.0126-0.2727-0.0042-0.03890.26630.02670.00750.36730.0160.1812-13.431869.7323-51.715
90.35420.0035-0.05040.12-0.22660.12980.10440.1632-0.0372-0.0048-0.03840.114-0.0128-0.11070.39360.40510.20770.03190.24650.10520.2171-7.49436.1511-32.5872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 9:182)
2X-RAY DIFFRACTION2(chain B and resseq 7:179)
3X-RAY DIFFRACTION3(chain C and resseq 7:180)
4X-RAY DIFFRACTION4(chain D and resseq 6:180)
5X-RAY DIFFRACTION5(chain E and resseq 5:180)
6X-RAY DIFFRACTION6(chain F and resseq 6:180)
7X-RAY DIFFRACTION7(chain G and resseq 8:181)
8X-RAY DIFFRACTION8(chain H and resseq 8:180)
9X-RAY DIFFRACTION9(chain A and resseq 201:203) or (chain H and resseq 201:203) or (chain E and resseq 201:201) or (chain D and resseq 201:201) or (chain G and resseq 201:202)

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