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- PDB-2qfc: Crystal Structure of Bacillus thuringiensis PlcR complexed with PapR -

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Basic information

Entry
Database: PDB / ID: 2qfc
TitleCrystal Structure of Bacillus thuringiensis PlcR complexed with PapR
Components
  • C-terminus pentapeptide from PapR protein
  • PlcR proteinBacillus cereus
KeywordsTRANSCRIPTION REGULATION / TPR / HTH
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
Bacillus PapR / Bacillus PapR protein / PlcR, tetratricopeptide repeat / RNPP family C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetratricopeptide repeat domain / Lambda repressor-like, DNA-binding domain superfamily ...Bacillus PapR / Bacillus PapR protein / PlcR, tetratricopeptide repeat / RNPP family C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetratricopeptide repeat domain / Lambda repressor-like, DNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PapR protein / Transcriptional activator plcR / PlcR protein
Similarity search - Component
Biological speciesBacillus thuringiensis serovar israelensis ATCC 35646 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsDeclerck, N. / Chaix, D. / Rugani, N. / Hoh, F. / Arold, S.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of PlcR: Insights into virulence regulation and evolution of quorum sensing in Gram-positive bacteria
Authors: Declerck, N. / Bouillaut, L. / Chaix, D. / Rugani, N. / Slamti, L. / Hoh, F. / Lereclus, D. / Arold, S.T.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PlcR protein
B: PlcR protein
C: C-terminus pentapeptide from PapR protein
D: C-terminus pentapeptide from PapR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8518
Polymers71,4264
Non-polymers4244
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.680, 85.680, 189.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein PlcR protein / Bacillus cereus


Mass: 35061.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar israelensis ATCC 35646 (bacteria)
Species: Bacillus thuringiensis / Strain: serovar israelensis ATCC 35646 / Gene: plcR / Plasmid: pET 16.28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q45782, UniProt: Q3EZ40*PLUS
#2: Protein/peptide C-terminus pentapeptide from PapR protein


Mass: 651.749 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide derived from the C-terminus of PapR
References: UniProt: Q3EZ39*PLUS
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 40% PEG 200, 100 mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.976
SYNCHROTRONESRF ID2920.979
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDDec 3, 2004ondulator
ADSC QUANTUM 3152CCDDec 4, 2004ondulator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.9791
ReflectionRedundancy: 8.3 % / Av σ(I) over netI: 4.2 / Number: 163226 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / D res high: 2.8 Å / D res low: 74.329 Å / Num. obs: 19572 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.8574.3399.710.0860.0867.8
6.268.8510010.0820.0829.1
5.116.2610010.0980.0989
4.435.1110010.0830.0838.6
3.964.4310010.0880.0888.5
3.613.9610010.120.128.4
3.353.6110010.1620.1628.3
3.133.3510010.2490.2498
2.953.1310010.4250.4258.1
2.82.9510010.6860.6868
ReflectionResolution: 2.6→74.2 Å / Num. obs: 24242 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.6 / Num. measured all: 19692 / Num. unique all: 3508 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→74.12 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.87 / SU B: 25.107 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic and TCL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.727 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1234 5.1 %RANDOM
Rwork0.224 ---
obs0.228 24186 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.09 Å20 Å2
2---0.19 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→74.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 28 30 4920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224980
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9746682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.645574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.28225260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.47615972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951522
X-RAY DIFFRACTIONr_chiral_restr0.1270.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023704
X-RAY DIFFRACTIONr_nbd_refined0.2490.22397
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2181
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.26
X-RAY DIFFRACTIONr_mcbond_it0.8291.52982
X-RAY DIFFRACTIONr_mcangle_it1.38924634
X-RAY DIFFRACTIONr_scbond_it2.29732318
X-RAY DIFFRACTIONr_scangle_it3.5854.52048
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 89 -
Rwork0.272 1691 -
obs-1780 100 %
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)
11.94211.6567-0.654215.98324.113320.26981.71350.7472-0.218-0.361-0.4352-1.73040.49931.655-1.27830.15530.3258-0.19040.9258-0.19650.340319.732667.276927.1747
218.8803-3.44792.05133.83620.27598.749-0.6584-1.229-1.1331.03080.8473-0.50091.2121.0101-0.18890.59510.2929-0.17270.2308-0.01430.27160.785259.534812.4855
30.5194-0.89171.40595.50890.02315.2978-0.10260.08890.12170.05990.1926-0.3672-0.23290.1212-0.090.1797-0.03260.00350.1202-0.05360.174-7.56368.10780.5538
44.15670.3740.19576.07330.32932.9369-0.1458-0.0782-0.2612-0.57350.2794-0.64850.35160.1048-0.13360.3305-0.02550.0390.1262-0.02290.1812-7.743653.5407-7.9221
53.18420.00611.46343.4172-1.43127.8744-0.1474-0.1845-0.3018-0.49150.04440.41810.3039-0.33020.1030.0983-0.0858-0.14860.12540.09490.2217-23.001541.2788-2.4904
615.71257.6886-3.50516.5863-0.63274.0067-1.72730.63451.32770.39920.54131.8763-2.9732-1.86231.1860.43610.3454-0.25970.5275-0.07430.5468-32.834948.24796.1771
716.7854-1.6379-5.46988.47874.398411.96760.75740.17471.18721.17620.0667-0.3273-1.03340.7576-0.82410.9161-0.19050.25140.12840.04440.116825.298957.5689-6.1884
87.831412.8204-5.303737.3996-7.16498.57760.25190.48370.5838-2.20290.09860.5769-1.0872-0.9077-0.35040.45210.36470.09680.01450.1527-0.00619.587645.61918.604
93.7381-1.6339-0.3154.2174-1.52594.56810.0920.02910.2273-0.30220.0254-0.23120.03050.371-0.11740.09250.02890.04820.2493-0.03910.170612.403933.606120.7806
105.5024-0.06310.79812.25170.22342.1229-0.2138-0.49440.1462-0.1320.2780.18390.0019-0.2294-0.06420.1136-0.01760.02260.18690.10130.141-11.322236.481725.967
1122.6297.85661.833318.4486-1.33910.39682.3912-1.4985-1.90310.2796-2.1411.31341.98661.1362-0.25020.84610.1138-0.0587-0.08390.20260.4928-17.302621.385815.0763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 603 - 60
2X-RAY DIFFRACTION2AA61 - 9161 - 91
3X-RAY DIFFRACTION3AA92 - 14192 - 141
4X-RAY DIFFRACTION4AA142 - 193142 - 193
5X-RAY DIFFRACTION5AA194 - 269194 - 269
6X-RAY DIFFRACTION6AA270 - 286270 - 286
7X-RAY DIFFRACTION7BB3 - 593 - 59
8X-RAY DIFFRACTION8BB60 - 9160 - 91
9X-RAY DIFFRACTION9BB92 - 14192 - 141
10X-RAY DIFFRACTION10BB142 - 269142 - 269
11X-RAY DIFFRACTION11BB270 - 286270 - 286

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