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- PDB-6x6f: The structure of Pf6r from the filamentous phage Pf6 of Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 6x6f
TitleThe structure of Pf6r from the filamentous phage Pf6 of Pseudomonas aeruginosa PA01
ComponentsPf6r
KeywordsDNA BINDING PROTEIN
Function / homologyNITRATE ION
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.735 Å
AuthorsMichie, K.A. / Norrian, P. / Duggin, I.G. / McDougald, D. / Rice, S.A.
Funding support Singapore, Australia, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
Australian Research Council (ARC)FT160100010 Australia
CitationJournal: Viruses / Year: 2021
Title: The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression.
Authors: Ismail, M.H. / Michie, K.A. / Goh, Y.F. / Noorian, P. / Kjelleberg, S. / Duggin, I.G. / McDougald, D. / Rice, S.A.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pf6r
B: Pf6r
C: Pf6r
D: Pf6r
F: Pf6r
H: Pf6r
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7649
Polymers66,5786
Non-polymers1863
Water6,810378
1
A: Pf6r
B: Pf6r


Theoretical massNumber of molelcules
Total (without water)22,1932
Polymers22,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-12 kcal/mol
Surface area9220 Å2
MethodPISA
2
C: Pf6r
D: Pf6r
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3795
Polymers22,1932
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-11 kcal/mol
Surface area7860 Å2
MethodPISA
3
F: Pf6r
H: Pf6r


Theoretical massNumber of molelcules
Total (without water)22,1932
Polymers22,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.880, 160.310, 45.670
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pf6r


Mass: 11096.414 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta T1R
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 20% Polyethylene glycol mono-methyl ether 5000, 200 mM Ammonium nitrate 10 mM HEPES, ph 7.5, 150 mM NaCl, 5% glycerol, 1 mM TCEP. 25% PEG 200 final cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 26, 2018
RadiationMonochromator: silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.735→40.95 Å / Num. obs: 59270 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.061 / Rrim(I) all: 0.087 / Net I/σ(I): 12.3
Reflection shellResolution: 1.735→1.797 Å / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique obs: 5818 / CC1/2: 0.751 / CC star: 0.926 / Rpim(I) all: 0.522 / Rrim(I) all: 0.742 / % possible all: 97.52

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WNM

6wnm


Resolution: 1.735→40.95 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 1953 -random selection
Rwork0.1728 ---
obs0.1736 59242 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.735→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 12 378 4364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054168
X-RAY DIFFRACTIONf_angle_d0.8545636
X-RAY DIFFRACTIONf_dihedral_angle_d12.4482564
X-RAY DIFFRACTIONf_chiral_restr0.048601
X-RAY DIFFRACTIONf_plane_restr0.006738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.735-1.77840.27491320.26214008X-RAY DIFFRACTION97
1.7784-1.82650.25381240.23434098X-RAY DIFFRACTION99
1.8265-1.88020.22261470.21684036X-RAY DIFFRACTION99
1.8802-1.94090.24221400.19574056X-RAY DIFFRACTION99
1.9409-2.01030.22531350.18794097X-RAY DIFFRACTION99
2.0103-2.09070.20151410.17494104X-RAY DIFFRACTION100
2.0907-2.18590.24891500.16864069X-RAY DIFFRACTION100
2.1859-2.30110.19461480.15454087X-RAY DIFFRACTION100
2.3011-2.44530.16141370.14784089X-RAY DIFFRACTION100
2.4453-2.63410.19671380.15724131X-RAY DIFFRACTION100
2.6341-2.89910.19581370.17464099X-RAY DIFFRACTION100
2.8991-3.31840.17771370.17184114X-RAY DIFFRACTION100
3.3184-4.18020.1991430.15884149X-RAY DIFFRACTION100
4.1802-40.950.17021440.16944152X-RAY DIFFRACTION100
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)
12.75160.6731-0.41986.62121.55393.5554-0.22830.159-0.09190.0933-0.1580.55010.5856-0.424-0.14590.1049-0.04210.0060.1491-0.04850.186-6.2081-25.2259-34.1688
25.0906-3.54171.87786.6874-1.76236.0901-0.1368-0.2305-0.21860.2788-0.02860.02220.48080.04640.08710.2057-0.01030.02650.0867-0.01960.13833.3646-22.7327-22.4825
31.60321.1758-0.07095.14540.64421.0513-0.08390.0841-0.07290.1985-0.01150.12830.213-0.14020.04370.1571-0.03050.03750.1471-0.03060.1083-1.3629-28.2141-33.1483
44.28774.68970.0077.5993-2.12318.30980.2111-0.43390.6185-0.29130.01720.5533-0.13-0.3105-0.22460.203-0.03770.05610.1795-0.05720.2334-17.9081-36.6602-27.7565
52.5692-1.1223-0.9992.72852.39922.5456-0.3056-0.0594-0.15050.04970.0403-0.22690.3940.18170.16320.2311-0.03050.05140.1356-0.0170.207312.0811-33.4267-43.3615
66.6418-0.40523.34275.3206-2.01366.1162-0.05380.3059-0.5182-0.42840.08750.26720.4041-0.58160.03240.2812-0.08550.02950.2712-0.0380.13095.0505-29.3588-55.8739
71.4431-0.0895-0.47022.6765-0.57111.6152-0.07180.1312-0.0838-0.1510.0673-0.12760.0856-0.1117-0.01190.2081-0.0380.04210.1585-0.04580.1367.067-29.6587-45.4703
84.0861-2.26790.08487.93991.80484.46520.0560.1972-0.2767-0.12060.0235-0.3673-0.00870.0456-0.02170.2189-0.05330.0420.1226-0.02920.22328.9045-48.865-40.9215
94.9216-0.6186-0.63741.5749-0.13483.7979-0.01940.022-0.21190.0038-0.08310.22840.1342-0.13590.00940.0819-0.0029-0.03180.0929-0.00080.0846-2.3918-11.45478.3128
101.58640.88180.08176.78412.05134.06880.0671-0.1271-0.01330.0916-0.04940.0225-0.0009-0.0473-0.01050.0640.0048-0.00410.1365-0.00290.1033-10.2807-1.68678.4219
112.93360.17880.61681.79370.62011.82830.0308-0.0725-0.00140.1278-0.0301-0.20350.1122-0.0169-0.00690.0879-0.0038-0.01410.1198-0.01240.10190.1148-5.67954.5712
124.49071.51070.88033.49780.78370.2550.0332-0.48670.08210.96140.3123-0.370.21350.15210.10320.27720.0722-0.14160.2917-0.03620.271312.5597-10.447512.0282
134.74121.0008-1.39881.9681.08245.11440.0846-0.18320.2412-0.08530.0667-0.1367-0.330.3568-0.11560.0919-0.0112-0.00510.1064-0.00340.11756.2158-2.0473-9.9407
142.6892-1.4076-1.74136.3461.49812.869-0.01490.0532-0.0163-0.12910.0039-0.03160.04140.04830.01060.1042-0.0062-0.01990.1616-0.00380.09690.3095-9.9267-14.3217
152.97040.99540.47862.7690.31461.25370.08150.01260.04630.0971-0.0337-0.5219-0.08480.6145-0.03870.1483-0.0365-0.0160.3369-0.01510.242312.5087-6.24-2.7731
162.0017-2.4031-0.41515.17443.11843.1020.1359-0.06220.07570.45110.0749-0.1909-0.61840.0576-0.19130.29030.05210.0250.14410.02570.163918.736619.446933.1474
175.6362-0.6887-0.49392.95051.39270.97180.0886-0.04570.22250.1772-0.05530.1393-0.2348-0.3716-0.04610.31760.07960.08670.21890.04270.14978.436213.003436.4642
181.0501-0.0048-0.51452.3253-0.02531.8421-0.0260.02080.04380.03140.14230.0082-0.2425-0.1868-0.09470.24020.05570.05680.16040.0140.153514.380417.83327.4577
195.1295-4.55213.85848.2773-0.85374.7269-0.04860.37460.3615-0.2380.0445-0.4319-0.43590.03510.05220.33760.02490.06980.17770.03430.214718.468331.965522.5206
205.27183.063.07361.92511.05246.27290.0242-0.35050.24760.8313-0.205-0.002-0.0514-0.09920.14660.3690.07670.00730.1803-0.00810.147318.796637.310334.522
212.8313-0.31060.4473.0485-0.38653.26560.27630.01820.2056-0.286-0.03380.3098-0.3174-0.4108-0.15220.16920.049-0.00630.11780.02360.126614.902111.226412.833
224.77931.7152-1.06365.6133-0.98212.34570.13050.04920.1633-0.1534-0.0385-0.0393-0.2309-0.0455-0.02090.12130.01880.01330.0693-0.00820.092926.14135.795814.2705
234.68985.01542.22426.78293.17075.20030.1006-0.3590.12870.79910.14210.38350.1465-0.08880.17920.12470.00210.00470.12480.04740.157915.25542.942621.1843
242.3394-1.60.88384.2362-1.22961.508-0.00660.00680.2597-0.14360.0349-0.219-0.3575-0.14510.01470.27050.04780.05180.13920.00940.136618.502820.922215.283
256.3304-1.92352.64847.3714-5.68436.1735-0.04410.4127-0.4672-0.65430.02360.45250.8980.0862-0.02840.39180.06380.02410.18460.00550.21112.900522.6884-0.2247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 85 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 27 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 62 )
8X-RAY DIFFRACTION8chain 'B' and (resid 63 through 85 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 15 )
10X-RAY DIFFRACTION10chain 'C' and (resid 16 through 36 )
11X-RAY DIFFRACTION11chain 'C' and (resid 37 through 62 )
12X-RAY DIFFRACTION12chain 'C' and (resid 63 through 77 )
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 15 )
14X-RAY DIFFRACTION14chain 'D' and (resid 16 through 42 )
15X-RAY DIFFRACTION15chain 'D' and (resid 43 through 77 )
16X-RAY DIFFRACTION16chain 'F' and (resid 2 through 15 )
17X-RAY DIFFRACTION17chain 'F' and (resid 16 through 36 )
18X-RAY DIFFRACTION18chain 'F' and (resid 37 through 62 )
19X-RAY DIFFRACTION19chain 'F' and (resid 63 through 73 )
20X-RAY DIFFRACTION20chain 'F' and (resid 74 through 85 )
21X-RAY DIFFRACTION21chain 'H' and (resid 2 through 15 )
22X-RAY DIFFRACTION22chain 'H' and (resid 16 through 36 )
23X-RAY DIFFRACTION23chain 'H' and (resid 37 through 42 )
24X-RAY DIFFRACTION24chain 'H' and (resid 43 through 73 )
25X-RAY DIFFRACTION25chain 'H' and (resid 74 through 85 )

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