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- PDB-6dgg: Cronobacter turicensis RpfR quorum-sensing receptor PAS domain in... -

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Basic information

Entry
Database: PDB / ID: 6dgg
TitleCronobacter turicensis RpfR quorum-sensing receptor PAS domain in complex with C12:0
ComponentsRpfR
KeywordsUNKNOWN FUNCTION / quorum sensing / diffusible signal factor / diguanylate cyclase / phosphodiesterase
Function / homology
Function and homology information


Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain ...Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / Nucleotide cyclase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
LAURIC ACID / Protein gmr
Similarity search - Component
Biological speciesCronobacter turicensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsWaldron, E.J. / Neiditch, M.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI125452 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110444 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI125185 United States
CitationJournal: PLoS Biol. / Year: 2019
Title: Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF.
Authors: Waldron, E.J. / Snyder, D. / Fernandez, N.L. / Sileo, E. / Inoyama, D. / Freundlich, J.S. / Waters, C.M. / Cooper, V.S. / Neiditch, M.B.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Mar 27, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RpfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8072
Polymers12,6061
Non-polymers2001
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.682, 29.131, 41.493
Angle α, β, γ (deg.)90.000, 115.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RpfR / Protein gmr


Mass: 12606.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cronobacter turicensis (strain DSM 18703 / LMG 23827 / z3032) (bacteria)
Strain: DSM 18703 / LMG 23827 / z3032 / Gene: gmr, Ctu_23300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9XTL5
#2: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.72 Å3/Da / Density % sol: 28.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 200 mM sodium formate, 18% (vol/vol) PEG 3350, 100 mM HEPES (pH 7.75), 1mM BDSF and 0.62% (vol/vol) DMSO

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.498→50 Å / Num. obs: 13614 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 9.32 Å2 / CC1/2: 0.928 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Χ2: 0.498 / Net I/σ(I): 9.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.498-1.532.70.2216500.9280.1520.2690.55892.3
1.53-1.552.80.1956420.9420.1350.2380.48395.3
1.55-1.5830.2086620.9520.1390.2510.5195.3
1.58-1.623.10.2226680.9390.1490.2680.5196.3
1.62-1.653.10.2026690.9450.1380.2460.48698.1
1.65-1.693.20.177000.9660.1140.2060.52397.4
1.69-1.733.10.1556730.970.1040.1870.46797.1
1.73-1.782.90.1446300.970.0990.1760.49793.6
1.78-1.833.20.1387020.9740.0910.1660.49197.8
1.83-1.893.50.1226840.9780.0760.1450.5199.3
1.89-1.963.50.1056960.9830.0660.1250.51299.6
1.96-2.043.50.0886630.9890.0550.1040.4898.2
2.04-2.133.50.0817050.9910.0510.0960.52299.3
2.13-2.243.50.0756870.9920.0470.0890.49198
2.24-2.383.40.0676680.9920.0430.080.46995.7
2.38-2.5630.0546730.9940.0380.0670.43895.3
2.56-2.823.50.0556960.9940.0350.0660.44499.1
2.82-3.233.50.0487140.9950.0310.0580.48399.6
3.23-4.073.40.0417060.9960.0260.0490.50899.3
4.07-503.30.0387260.9970.0250.0460.57596.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU1

5iu1


Resolution: 1.498→37.517 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.79
RfactorNum. reflection% reflection
Rfree0.1743 1314 9.94 %
Rwork0.147 --
obs0.1498 13221 94.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.59 Å2 / Biso mean: 16.4561 Å2 / Biso min: 4.11 Å2
Refinement stepCycle: final / Resolution: 1.498→37.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 37 89 967
Biso mean--24.85 24.34 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005872
X-RAY DIFFRACTIONf_angle_d0.8931168
X-RAY DIFFRACTIONf_chiral_restr0.077127
X-RAY DIFFRACTIONf_plane_restr0.005151
X-RAY DIFFRACTIONf_dihedral_angle_d23.54330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4981-1.5580.23511340.18461163129785
1.558-1.6290.22341340.17921267140191
1.629-1.71480.21781420.16681287142992
1.7148-1.82230.21951420.15941300144293
1.8223-1.9630.16951530.14411364151798
1.963-2.16050.15171490.13081364151398
2.1605-2.47310.18231440.12831347149196
2.4731-3.11560.16321570.14391394155198
3.1156-37.52920.15171590.14651421158098
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)
12.3842-0.45750.06412.72120.21012.1743-0.02480.0819-0.0407-0.09140.04170.09740.174-0.0412-0.01710.0866-0.0104-0.01030.0353-0.00010.0553.98334.58838.4479
27.8009-7.199-0.97297.7604-0.31291.79760.22280.18580.3218-0.3443-0.202-0.35250.12590.1213-0.02280.1158-0.01050.02390.07240.00030.080815.870312.29050.6806
33.37210.36671.91333.8196-0.58982.4208-0.01660.13460.0522-0.12580.04750.1707-0.04290.0373-0.01510.11150.00450.01350.0364-0.01450.02288.761515.667910.3837
42.8838-1.1323-0.54734.10991.0992.4251-0.01510.079-0.13290.02690.0092-0.01170.16270.04740.00380.0849-0.01130.01040.03270.00490.025512.240710.230412.9788
58.74616.654-7.68815.1208-6.11528.2021-0.0614-0.3261-0.31060.48120.19350.4291-0.1489-0.0855-0.06910.21240.05170.08350.12760.07390.2152.54375.315526.6541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 123 through 162 )A123 - 162
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 179 )A163 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 193 )A180 - 193
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 224 )A194 - 224
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 122 )A116 - 122

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