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

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Basic information

Entry
Database: PDB / ID: 6ovk
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
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
TonB-dependent receptor-like / FecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / 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-like / FecR, N-terminal / Domain of unknown function (DUF4880) / FecR protein / Fe(2+)-dicitrate sensor, transmembrane component / FecR protein / 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 Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily
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 / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsJensen, J.L. / Colbert, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)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
Revision 1.4Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
R: Siderophore-interacting protein
B: Ferric-pseudobactin BN7/BN8 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5584
Polymers32,2582
Non-polymers3002
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-6 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.385, 44.558, 141.009
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: 24152.422 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.: 319 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 150mM ammonium tartrate dibasic, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→44.558 Å / Num. obs: 27017 / % possible obs: 96.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Net I/σ(I): 25.2
Reflection shellResolution: 1.761→1.761 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 274 / CC1/2: 0.966 / Rpim(I) all: 0.11 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
SCALAdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OVM

6ovm


Resolution: 1.761→42.487 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.44
RfactorNum. reflection% reflection
Rfree0.2093 1337 4.95 %
Rwork0.1599 --
obs0.1624 27017 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.761→42.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 20 319 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112412
X-RAY DIFFRACTIONf_angle_d1.2133313
X-RAY DIFFRACTIONf_dihedral_angle_d16.9111468
X-RAY DIFFRACTIONf_chiral_restr0.074383
X-RAY DIFFRACTIONf_plane_restr0.007442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7606-1.82350.24751320.18282609X-RAY DIFFRACTION100
1.8235-1.89660.21751250.17082622X-RAY DIFFRACTION100
1.8966-1.98290.22981280.16162615X-RAY DIFFRACTION100
1.9829-2.08740.22471340.16172299X-RAY DIFFRACTION88
2.0874-2.21820.21571350.15942628X-RAY DIFFRACTION100
2.2182-2.38940.20681290.16852408X-RAY DIFFRACTION92
2.3894-2.62990.22341270.17582654X-RAY DIFFRACTION100
2.6299-3.01030.25531300.17832458X-RAY DIFFRACTION92
3.0103-3.79230.19781490.15182597X-RAY DIFFRACTION97
3.7923-42.49960.17181480.14052790X-RAY DIFFRACTION98
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)
12.1253-1.08861.02743.6484-1.03061.95890.04880.2111-0.42-0.0835-0.05990.06910.20750.10180.03010.131-0.01050.00050.077-0.0310.19311.6089-20.5847-26.5202
22.2731-0.273-0.47681.18030.91261.666-0.0838-0.0531-0.01420.03680.0249-0.0419-0.00880.27510.05460.1145-0.0296-0.01090.11150.02170.092113.241-13.7733-23.3616
32.421.1779-0.54643.67030.19144.35020.1598-0.04520.129-0.11490.2806-0.3008-0.38420.2108-0.27690.2125-0.1111-0.00240.1324-0.01830.192516.4998-2.5255-23.7076
44.68251.36483.96390.88131.2143.89560.164-0.3448-0.09450.20720.01670.0644-0.13540.1212-0.14830.169-0.005-0.0030.0888-0.01110.10892.0223-8.0278-13.1378
51.87-0.16430.22552.2308-0.25162.0651-0.02220.11930.1115-0.09380.0016-0.0298-0.13440.1330.02590.1057-0.02340.00830.08190.01510.0978-4.21095.3513-22.8644
61.89460.20121.03451.21060.31153.1956-0.147-0.02510.1912-0.07030.07780.1205-0.4583-0.28210.02080.12770.014-0.00480.0996-0.00660.1135-12.21768.2678-21.0507
78.7413.308-0.75665.08490.37993.23970.0153-0.5982-0.5290.1213-0.04750.26820.5838-0.1790.00530.1951-0.0114-0.01330.35980.08690.2029-3.3593-4.90672.3907
83.76560.16810.27451.93720.30242.7083-0.0588-0.4681-0.0758-0.1237-0.00380.08640.1512-0.09550.09230.09310.00460.00820.133-0.01530.0672-3.94051.1534-5.733
92.5657-1.77223.4783.9703-2.83896.2658-0.2294-0.35470.45130.0626-0.09610.0358-0.32470.58320.22730.1724-0.0574-0.02920.2861-0.07710.1691.906810.2454-1.36
103.9770.43090.70036.65490.82453.36210.0831-0.5354-0.22270.355-0.020.32840.2309-0.338-0.03780.1809-0.01920.02880.34390.05610.1375-7.7666-2.08135.0013
114.99250.0527-0.12194.3978-0.54047.910.1652-0.23820.0128-0.0098-0.26190.5859-0.0943-0.1730.12840.1697-0.01280.01590.2151-0.07510.1853-7.61799.10672.2321
122.9715-1.7644-1.65421.04690.98240.9205-0.0870.6-0.3133-0.3691-0.0550.4725-0.2153-0.83790.18450.3098-0.0399-0.08430.5585-0.11660.6284-18.44644.4107-7.7709
131.6894-0.747-0.20184.8521.68384.1321-0.2772-0.1921-0.03780.3689-0.10620.387-0.0731-0.40850.43440.15380.02170.00140.2711-0.08220.2274-10.928212.90781.8331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'R' and (resid 111 through 149 )
2X-RAY DIFFRACTION2chain 'R' and (resid 150 through 224 )
3X-RAY DIFFRACTION3chain 'R' and (resid 225 through 239 )
4X-RAY DIFFRACTION4chain 'R' and (resid 240 through 250 )
5X-RAY DIFFRACTION5chain 'R' and (resid 251 through 283 )
6X-RAY DIFFRACTION6chain 'R' and (resid 284 through 323 )
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 78 )
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 103 )
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 113 )
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 118 )
13X-RAY DIFFRACTION13chain 'B' and (resid 119 through 128 )

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