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- PDB-7xro: LysR-family transcriptional regulator RipR effector binding domai... -

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Basic information

Entry
Database: PDB / ID: 7xro
TitleLysR-family transcriptional regulator RipR effector binding domain with its effector, 3-phenylpropionic acid
ComponentsRipR
KeywordsTRANSCRIPTION / LTTR / host-pathogen interaction
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
HTH-type transcriptional regulator BudR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GLYCINE / HYDROCINNAMIC ACID / Hca operon transcriptional activator HcaR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKi, N. / Ha, N.-C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The activation mechanism of the itaconic acid-responsive LTTR RipR in the pathogenesis of the foodborne-pathogen Salmonella enterica
Authors: Ki, N. / Ha, N.-C.
History
DepositionMay 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
B: RipR
C: RipR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5807
Polymers45,2082
Non-polymers3715
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-17 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.107, 83.107, 172.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RipR / Itaconate degradation transcriptional regulator RipR / LysR family transcriptional regulator / ...Itaconate degradation transcriptional regulator RipR / LysR family transcriptional regulator / Putative transcriptional regulator


Mass: 22604.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Gene: stmR, hcaR_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RQ20
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 286.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate trihydrate (pH 6.5), 1.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.8→28.7 Å / Num. obs: 17475 / % possible obs: 99.4 % / Redundancy: 19.6 % / Biso Wilson estimate: 86.29 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.095 / Rsym value: 0.093 / Net I/av σ(I): 7.8 / Net I/σ(I): 26.8 / Num. measured all: 341941
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.9518.71.6970.54718525250.3981.7441.6972.199.5
2.95-3.1319.91.0540.74660823470.2381.0821.0543.599
3.13-3.3521.40.6061.34786122410.1320.6210.6066.499.6
3.35-3.6120.80.2642.94392421100.0580.270.26413.599.7
3.61-3.9620.30.1485.23861219060.0330.1510.14822.799.7
3.96-4.4319.40.089.43448117730.0180.0820.0837.399.8
4.43-5.1118.30.05213.52877715690.0130.0540.05254.299.8
5.11-6.2616.50.04814.32201013340.0120.0490.04849.898.7
6.26-8.8520.20.0320.72144410620.0070.030.0380.499.6
8.85-28.718.20.02129110396080.0050.0210.021106.595.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
PHENIX1.20.1_4487phasing
HKL-2000v722data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V5V

7v5v


Resolution: 2.8→28.7 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 1739 9.97 %
Rwork0.2133 15703 -
obs0.2177 17442 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.11 Å2 / Biso mean: 102.6834 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.8→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 21 26 3186
Biso mean--103.02 89.82 -
Num. residues----410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.880.36761450.3281312145799
2.88-2.980.38041420.3361261140398
2.98-3.080.35411420.33471283142599
3.08-3.20.40941400.31211277141799
3.21-3.350.35541440.29631298144299
3.35-3.530.32471410.26891289143099
3.53-3.750.28411440.24491300144499
3.75-4.040.26621410.22051293143499
4.04-4.440.24791500.194713231473100
4.44-5.080.18781510.16613171468100
5.08-6.390.25341470.19961343149099
6.39-28.70.20191520.16941407155998
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)
17.0115-0.4808-2.91443.998-0.18637.2803-0.4317-0.0387-0.08590.08390.3084-0.19030.5632-0.34970.11060.5324-0.0431-0.01140.44280.04310.405-29.005126.1197-46.116
24.2161.14783.41095.8961-0.79787.06410.3960.34380.7111-0.063-0.05890.0627-1.2788-1.2175-0.30790.83520.17470.36521.02530.1471.0678-46.793942.3633-35.9308
33.3375-0.7109-1.96741.6340.63166.83990.28970.23450.2769-0.1095-0.05370.2434-0.2474-1.4854-0.21090.4794-0.07760.0650.81170.11530.5805-40.002729.7982-42.3261
41.6968-2.0202-1.55899.46090.94679.570.2477-0.53570.56260.2229-0.3306-0.38420.13950.93840.26330.5108-0.22490.10621.0050.0030.7417-37.520237.645-15.5917
53.0229-1.4170.49346.96832.48016.77940.4593-0.8789-0.44060.6094-0.4944-0.24132.4012-0.9770.07271.4884-0.27520.06711.04130.25950.7502-36.668613.4963-21.6494
67.8986-3.11233.36448.001-1.13086.47670.1668-1.12-0.14910.51160.2655-0.61942.12050.3219-0.32551.1160.03570.06921.00070.06480.5848-26.872817.4977-26.4396
72.205-1.3358-2.50264.30370.98487.9276-0.031-0.5970.02080.35240.0801-0.24520.98810.21340.05610.7497-0.15690.07751.12040.150.6571-38.86724.7406-18.0257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 85 through 172 )B85 - 172
2X-RAY DIFFRACTION2chain 'B' and (resid 173 through 229 )B173 - 229
3X-RAY DIFFRACTION3chain 'B' and (resid 230 through 291 )B230 - 291
4X-RAY DIFFRACTION4chain 'C' and (resid 89 through 156 )C89 - 156
5X-RAY DIFFRACTION5chain 'C' and (resid 157 through 189 )C157 - 189
6X-RAY DIFFRACTION6chain 'C' and (resid 190 through 236 )C190 - 236
7X-RAY DIFFRACTION7chain 'C' and (resid 237 through 291 )C237 - 291

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