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- PDB-6wpz: The structure of Pf4r from a superinfective isolate of the filame... -

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Basic information

Entry
Database: PDB / ID: 6wpz
TitleThe structure of Pf4r from a superinfective isolate of the filamentous phage Pf4 of Pseudomonas aeruginosa PA01
ComponentsPf4r
KeywordsDNA BINDING PROTEIN
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.993 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
DepositionApr 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: Pf4r
B: Pf4r
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0293
Polymers20,9942
Non-polymers351
Water75742
1
A: Pf4r

A: Pf4r


Theoretical massNumber of molelcules
Total (without water)20,9942
Polymers20,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area8280 Å2
MethodPISA
2
B: Pf4r
hetero molecules

B: Pf4r
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, Gel filtration shows this protein is monomeric via gel filtration in a biological buffer., light scattering, MALS analysis also shows this protein is monomeric in a biological buffer.
  • 21.1 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)21,0654
Polymers20,9942
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area1830 Å2
ΔGint-27 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.444, 45.128, 168.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-101-

CL

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Components

#1: Protein Pf4r


Mass: 10496.806 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CGU42_23305 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Rosetta T1R
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.63 Å3/Da / Density % sol: 33.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Polyethylene glycol monomethyl ether 550 25% (v/v) 50 mM HEPES; pH 7.0 10 mM Magnesium chloride Protein at 50 mg/ml. Frozen in cryo protectant 20 % PEG200

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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: Feb 23, 2019
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: 1.98→39.93 Å / Num. obs: 9885 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.195 / Net I/σ(I): 4.6
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1 / Num. unique obs: 1417 / CC1/2: 0.513 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WNM

6wnm


Resolution: 1.993→28.353 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 989 10.01 %random
Rwork0.1858 ---
obs0.1903 9882 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.993→28.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 1 42 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041333
X-RAY DIFFRACTIONf_angle_d0.6551809
X-RAY DIFFRACTIONf_dihedral_angle_d2.019963
X-RAY DIFFRACTIONf_chiral_restr0.046201
X-RAY DIFFRACTIONf_plane_restr0.005230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9934-2.09850.28191380.2431238X-RAY DIFFRACTION99
2.0985-2.22990.28941410.21021265X-RAY DIFFRACTION100
2.2299-2.4020.25591390.19661254X-RAY DIFFRACTION100
2.402-2.64350.26171400.1791261X-RAY DIFFRACTION100
2.6435-3.02570.22471390.17561248X-RAY DIFFRACTION100
3.0257-3.81060.20571430.1741287X-RAY DIFFRACTION100
3.8106-28.3530.21181490.18041340X-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)
14.40232.2979-0.69562.5739-0.65323.3622-0.57250.33751.01330.13410.11170.6995-0.48620.05210.2140.3970.0099-0.04870.295-0.03720.29413.24734.3487-9.7639
22.7226-0.48451.19434.4627-0.35863.2812-0.0338-0.51570.48570.5258-0.26850.16010.4251-0.5180.2530.2953-0.08690.04920.4567-0.09530.3141-2.1491-7.7357-13.3241
33.73630.68510.13891.383-1.32541.82610.0871-0.63140.32480.0355-0.15490.93-0.0036-0.6910.2180.5309-0.11030.04750.4907-0.0850.50690.9877-4.0764-5.3758
42.3282-0.453-0.59912.264-0.86522.37470.0726-0.0166-0.0616-0.161-0.1166-0.02530.01250.2421-0.00760.3250.0092-0.02380.23070.02240.148614.9020.6214-5.7897
50.2559-0.43430.1633.70630.11645.51170.21010.16580.0255-0.4672-0.0209-0.2940.05380.1995-0.0020.4560.00770.02590.3438-0.00320.286119.3232.8006-17.2106
61.7131-0.1776-1.34031.45910.54244.73980.16340.1384-0.03750.0089-0.14770.1164-0.2283-0.24250.32340.29-0.0216-0.01140.20060.00450.27738.49768.0487-36.2929
73.32850.73540.48493.1033-0.25623.13320.2155-0.26770.19890.4058-0.09690.44840.0115-0.1844-0.07420.2236-0.00250.03680.179-0.02180.191713.869213.0619-25.693
81.3993-0.14740.55743.6803-0.78581.3906-0.21-0.01930.1448-0.10070.1552-0.04750.10750.01290.02130.2107-0.0142-0.00280.2207-0.02890.233516.737812.8881-35.3832
91.27390.6403-0.54890.3799-0.60521.5289-0.0639-0.0029-0.06950.08420.001-0.09860.0546-0.02280.04840.18430.0020.03540.1633-0.01280.202812.5761-3.2401-36.296
100.6568-0.4884-0.69240.37540.61040.91810.0786-0.1080.0930.09410.1369-0.01480.3739-0.1421-0.26790.41270.01030.03370.2538-0.02120.312114.2865-17.9856-31.5105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 15 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 34 )
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 51 )
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 78 )
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 95 )

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