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- PDB-6ovm: Crystal Structure of the Pseudomonas capeferrum Anti-sigma Regula... -

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Basic information

Entry
Database: PDB / ID: 6ovm
TitleCrystal Structure of the Pseudomonas capeferrum Anti-sigma Regulator PupR C-terminal Cell-surface Signaling Domain in Complex with the Outer Membrane Transporter PupB N-terminal Signaling Domain (SeMet)
Components
  • Ferric-pseudobactin BN7/BN8 receptor
  • Siderophore-interacting protein
KeywordsSIGNALING PROTEIN / transcriptional regulation / periplasmic protein / iron transport regulation
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity
Similarity search - Function
FecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / TonB-dependent receptor-like / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent siderophore receptor ...FecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / TonB-dependent receptor-like / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Siderophore-interacting protein / Ferric-pseudobactin BN7/BN8 receptor
Similarity search - Component
Biological speciesPseudomonas capeferrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsJensen, J.L. / Colbert, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM113227-01 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria.
Authors: Jensen, J.L. / Jernberg, B.D. / Sinha, S.C. / Colbert, C.L.
History
DepositionMay 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 13, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Siderophore-interacting protein
B: Ferric-pseudobactin BN7/BN8 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7464
Polymers32,4462
Non-polymers3002
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-7 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.574, 44.714, 141.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Siderophore-interacting protein / PupR protein


Mass: 24340.000 Da / Num. of mol.: 1 / Fragment: C-terminal Cell-surface Signaling Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas capeferrum (bacteria) / Gene: PC358_08100, pupR / Plasmid: pMBP-Parallel-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A084CH09
#2: Protein Ferric-pseudobactin BN7/BN8 receptor


Mass: 8105.890 Da / Num. of mol.: 1 / Fragment: N-terminal Signaling Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas capeferrum (bacteria) / Gene: PC358_08105, pupB / Plasmid: pGEXr / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: A0A084CH10
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200mM sodium potassium tartrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.51→141.34 Å / Num. obs: 68598 / % possible obs: 98 % / Redundancy: 5.9 % / CC1/2: 0.999 / Net I/σ(I): 18.9
Reflection shellResolution: 1.51→1.53 Å / Num. unique obs: 1511 / CC1/2: 0.765

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→42.63 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.61
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 3096 4.71 %RANDOM
Rwork0.1527 ---
obs0.1541 65715 93.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 20 357 2604
Refine LS restraintsType: f_angle_d / Dev ideal: 1.349 / Number: 3468
LS refinement shellResolution: 1.6→1.625 Å
RfactorNum. reflection% reflection
Rfree0.2165 93 -
Rwork0.1899 1943 -
obs--64 %
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)
10.9773-0.08370.34412.1068-0.46721.07090.0030.0696-0.2935-0.09210.0350.03270.17770.0342-0.03040.1108-0.03370.0233-0.0352-0.01580.263521.1831.133244.0501
21.8937-0.3528-0.01022.3983-0.1972.2099-0.04770.0284-0.31910.0607-0.0122-0.06780.2120.24150.03790.0947-0.0139-0.01770.0468-0.01170.140428.89782.627245.6973
31.90860.4191-1.38311.12980.23311.3214-0.07850.01050.0193-0.02530.0845-0.0727-0.09850.29480.01830.0796-0.0447-0.02460.09390.00840.084536.7511.152747.2158
40.64860.54430.29391.2660.37410.39150.0272-0.01240.0262-0.030.0219-0.1-0.14870.1053-0.03910.1817-0.1830.01520.0549-0.00760.120938.735619.840746.1891
55.56622.85995.49971.99022.6256.2360.1165-0.2489-0.05470.20160.01120.03660.0310.0452-0.1380.10240.0170.01350.0501-0.0180.089423.798114.286957.4538
60.93580.2773-0.07422.43990.14260.8347-0.0590.02990.0852-0.10130.0412-0.0089-0.13110.10040.00860.0656-0.02040.00040.05390.01050.085917.550626.962948.2401
73.0460.3180.27433.9790.15463.5372-0.051-0.05380.0863-0.0495-0.0130.1789-0.1392-0.15780.00770.02970.0037-00.0336-0.00820.059211.936726.768755.1746
82.74580.87920.66113.83640.80613.3039-0.1616-0.14490.43950.00170.0010.26-0.4839-0.24990.11120.12640.0223-0.03280.07410.00740.14447.323734.472144.2606
95.26451.4807-0.60024.19240.04782.1952-0.0089-0.4967-0.4610.2521-0.059-0.07540.3562-0.03410.0720.13560.00360.00790.22430.04830.090619.351117.416473.1425
102.74490.32730.15463.1405-0.10812.4093-0.07-0.2420.0696-0.0902-0.03520.0416-0.03270.01890.08430.0638-0.0042-0.00420.0822-0.02150.046218.153725.033564.8145
115.6716-3.33894.34863.611-4.04774.679-0.16730.06970.38690.2611-0.1088-0.2842-0.51880.52280.31150.1531-0.0389-0.01510.1732-0.04640.082124.956931.355571.4209
123.7679-0.46010.11428.7166-0.45085.0940.0208-0.3436-0.17220.27070.01620.48110.2657-0.3648-0.02330.0997-0.0120.01670.23160.04020.076513.982120.287175.7166
134.10120.9276-0.23232.3488-0.67275.25860.1027-0.51360.22910.473-0.0288-0.2859-0.44250.0011-0.06440.16090.001-0.0110.208-0.06050.109319.493232.036375.9488
146.60244.60765.85664.91542.00237.7526-0.03910.2474-0.3223-0.40110.0440.75560.2246-0.8492-0.02550.1874-0.019-0.03670.3585-0.1520.39167.360329.296367.4601
154.5121-2.3985-1.8086.39483.7335.2727-0.1303-0.0640.1080.7202-0.10590.17240.2878-0.36980.2160.15510.01160.02360.1512-0.04050.129110.589535.830573.025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'R' and (resid 111 through 132 )
2X-RAY DIFFRACTION2chain 'R' and (resid 133 through 171 )
3X-RAY DIFFRACTION3chain 'R' and (resid 172 through 224 )
4X-RAY DIFFRACTION4chain 'R' and (resid 225 through 239 )
5X-RAY DIFFRACTION5chain 'R' and (resid 240 through 250 )
6X-RAY DIFFRACTION6chain 'R' and (resid 251 through 283 )
7X-RAY DIFFRACTION7chain 'R' and (resid 284 through 305 )
8X-RAY DIFFRACTION8chain 'R' and (resid 306 through 323 )
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 81 )
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 89 )
12X-RAY DIFFRACTION12chain 'B' and (resid 90 through 103 )
13X-RAY DIFFRACTION13chain 'B' and (resid 104 through 108 )
14X-RAY DIFFRACTION14chain 'B' and (resid 109 through 118 )
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 128 )

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