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- PDB-6dgn: Cronobacter turicensis BDSF synthase RpfF in complex with the Rpf... -

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Basic information

Entry
Database: PDB / ID: 6dgn
TitleCronobacter turicensis BDSF synthase RpfF in complex with the RpfR quorum-sensing receptor FI domain
Components
  • RpfF
  • RpfR
KeywordsUNKNOWN FUNCTION / quorum sensing / diffusible signal factor / diguanylate cyclase / phosphodiesterase
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / isomerase activity
Similarity search - Function
Light-harvesting Protein - #30 / Light-harvesting Protein / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase ...Light-harvesting Protein - #30 / Light-harvesting Protein / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Other non-globular / Nucleotide cyclase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Special / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Enoyl-CoA hydratase/isomerase / cyclic-guanylate-specific phosphodiesterase
Similarity search - Component
Biological speciesBurkholderia cenocepacia PC184 (bacteria)
Cronobacter turicensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 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 1.1Mar 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RpfF
B: RpfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8917
Polymers42,4272
Non-polymers4635
Water2,648147
1
A: RpfF
B: RpfR
hetero molecules

A: RpfF
B: RpfR
hetero molecules

A: RpfF
B: RpfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,67321
Polymers127,2826
Non-polymers1,39015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13900 Å2
ΔGint-73 kcal/mol
Surface area40300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.939, 144.939, 116.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein RpfF / Enoyl-Coa hydratase/isomerase


Mass: 32088.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia PC184 (bacteria)
Gene: BCPG_03941 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2W0S6
#2: Protein RpfR / protein gmr


Mass: 10338.766 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium acetate (pH 5.6) and 250 mM ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 31951 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.825 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.034 / Rrim(I) all: 0.153 / Χ2: 0.62 / Net I/σ(I): 17.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.999-2.0321.11.57215730.8250.351.6110.445100
2.03-2.0720.61.21416000.830.2751.2450.73899.9
2.07-2.1120.91.2715740.8820.2841.3020.568100
2.11-2.1520.90.93715860.9270.2090.960.456100
2.15-2.220.80.80616120.9340.180.8260.462100
2.2-2.2520.40.73415710.9350.1670.7530.748100
2.25-2.3120.50.74515840.9580.1680.7640.538100
2.31-2.3720.50.53615790.970.1210.550.469100
2.37-2.4420.50.47115840.9770.1060.4830.471100
2.44-2.5220.30.39315750.9840.0890.4030.473100
2.52-2.6119.30.35715950.9840.0830.3670.49399.9
2.61-2.71180.35716060.9860.0860.3680.683100
2.71-2.8416.40.22215750.9920.0560.230.53799.9
2.84-2.9921.30.18316070.9960.040.1870.536100
2.99-3.1721.30.13316040.9980.0290.1360.57100
3.17-3.42210.09816000.9990.0220.1010.614100
3.42-3.7620.90.08515970.9990.0190.0870.903100
3.76-4.3119.90.06316100.9990.0140.0640.869100
4.31-5.4317.80.05116400.9990.0120.0530.84599.9
5.43-5021.30.051167910.0110.0520.96299.9

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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 / Resolution: 1.999→41.84 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.91
RfactorNum. reflection% reflection
Rfree0.2012 2000 6.26 %
Rwork0.1678 --
obs0.1699 31949 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.96 Å2 / Biso mean: 41.0608 Å2 / Biso min: 19.43 Å2
Refinement stepCycle: final / Resolution: 1.999→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 61 147 3063
Biso mean--66.19 40.2 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032942
X-RAY DIFFRACTIONf_angle_d0.5933982
X-RAY DIFFRACTIONf_chiral_restr0.042439
X-RAY DIFFRACTIONf_plane_restr0.003512
X-RAY DIFFRACTIONf_dihedral_angle_d16.341734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9993-2.04930.25611420.222221252267
2.0493-2.10470.27821410.247621122253
2.1047-2.16660.2041420.184121352277
2.1666-2.23650.25141420.190521112253
2.2365-2.31640.29221410.227421242265
2.3164-2.40920.19761420.170221212263
2.4092-2.51880.20871410.171721152256
2.5188-2.65160.21131430.165821402283
2.6516-2.81770.21571420.170221262268
2.8177-3.03520.20011430.160521432286
3.0352-3.34050.16471420.148121382280
3.3405-3.82360.17991450.141821662311
3.8236-4.81620.18321450.143221612306
4.8162-41.84940.19521490.182122322381
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)
12.3688-1.16591.20774.9972-0.44081.5919-0.1953-0.30360.81110.10480.0428-0.6472-0.69440.1320.14520.5446-0.0643-0.05670.30580.01710.44466.176338.276716.8518
22.0481-2.07650.49864.6839-0.12832.1829-0.18970.0490.4258-0.09670.03340.4058-0.4425-0.1587-0.00280.4337-0.0014-0.05140.2582-0.00130.2991-0.18432.128518.6492
33.3375-1.5768-0.04284.3927-0.54341.23280.62831.1439-0.073-0.9142-0.27250.1417-0.3401-0.0283-0.00150.58860.0344-0.09290.33810.04190.2555-0.377830.52756.5293
41.7528-0.5911.29321.46880.20722.55450.2270.01370.2959-0.2673-0.0653-0.1454-0.31730.1913-0.0170.3909-0.05860.02630.23260.02250.28289.620528.612614.4106
55.05051.55023.1220.93031.65063.4779-0.1479-0.31230.4439-0.1088-0.14050.2653-0.5094-0.53660.24790.40220.0889-0.02420.32110.02980.3233-17.356227.349915.8712
67.4131-0.47242.40381.49220.16183.27080.10740.31040.4147-0.1329-0.1072-0.0373-0.2834-0.14280.05230.29550.02630.02330.22740.00850.2065-9.826120.51356.2262
72.04120.39230.31811.36890.31220.79680.0147-0.2674-0.08530.1221-0.0358-0.0131-0.095-0.1135-0.01140.24960.0108-0.0160.24380.04070.2063-4.634116.431823.6595
81.40570.06510.74022.18971.07351.2833-0.002-0.03140.0012-0.13840.0355-0.2545-0.28140.093-0.06920.298-0.0610.00710.2430.01250.262612.6718.029219.6306
97.4996-1.6927-3.18062.09711.68084.12230.12790.1192-0.0276-0.0156-0.09460.181-0.3397-0.5199-0.02560.22510.0511-0.01670.22270.06490.1783-19.233717.263613.0524
102.51783.9563-1.16919.83343.75899.3259-0.5736-0.2443-0.61390.19070.8214-1.30440.53410.6636-0.33370.40910.0148-0.02320.5728-0.07340.502834.411714.212731.7614
112.00991.4768-1.14349.35553.86728.6252-0.18930.69170.6897-0.5261-0.1451-0.4812-0.69150.32080.32380.3144-0.0748-0.07440.4104-0.00110.268326.204729.114132.4449
123.4591-2.4044-0.12442.49962.34886.03310.0935-0.19440.4298-0.31070.0961-0.3065-0.37780.6117-0.19940.3169-0.0853-0.02010.3077-0.05870.362724.248825.434129.742
137.22610.46130.33416.23242.55465.52350.0162-1.05110.48320.7044-0.5194-0.3207-0.8891-0.47280.34940.6719-0.0273-0.16150.4365-0.08740.342821.530530.88142.2501
147.77310.03041.58963.4963-0.24819.1509-0.2305-0.52640.03230.3830.234-0.52120.22490.04830.16140.3637-0.0544-0.03380.3878-0.05390.382526.369522.37539.1719
155.7242-0.84251.65366.1721-0.91925.7388-0.54160.03451.1788-0.40310.1644-0.3792-0.48220.06470.40520.4342-0.1494-0.17270.3928-0.12750.629726.64831.5835.4306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )A2 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 45 )A27 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 61 )A46 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 73 )A62 - 73
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 96 )A74 - 96
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 115 )A97 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 211 )A116 - 211
8X-RAY DIFFRACTION8chain 'A' and (resid 212 through 241 )A212 - 241
9X-RAY DIFFRACTION9chain 'A' and (resid 242 through 277 )A242 - 277
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 19 )B5 - 19
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 24 )B20 - 24
12X-RAY DIFFRACTION12chain 'B' and (resid 25 through 47 )B25 - 47
13X-RAY DIFFRACTION13chain 'B' and (resid 48 through 61 )B48 - 61
14X-RAY DIFFRACTION14chain 'B' and (resid 62 through 85 )B62 - 85
15X-RAY DIFFRACTION15chain 'B' and (resid 86 through 95 )B86 - 95

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