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

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Basic information

Entry
Database: PDB / ID: 6wnm
TitleThe structure of Pf4r from a superinfective isolate of the filamentous phage Pf4 of Pseudomonas aeruginosa PA01
ComponentsPf4r
KeywordsDNA BINDING PROTEIN
Function / homologyChem-U5J
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 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 22, 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pf4r
B: Pf4r
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4773
Polymers20,9942
Non-polymers4841
Water1086
1
A: Pf4r
hetero molecules

A: Pf4r
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9614
Polymers20,9942
Non-polymers9682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area8530 Å2
MethodPISA
2
B: Pf4r

B: Pf4r


Theoretical massNumber of molelcules
Total (without water)20,9942
Polymers20,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1350 Å2
ΔGint-12 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.109, 47.477, 169.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 PAO1 (bacteria) / Plasmid: pNC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta T1R
#2: Chemical ChemComp-U5J / [(2R)-3-{[2-(carboxymethoxy)benzene-1-carbonyl]amino}-2-methoxypropyl](hydroxy)mercury


Mass: 483.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H17HgNO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.82 Å3/Da / Density % sol: 32.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mg/ml protein, 37% PEG 3350, 50 mM Tris, 5% glycerol, 50 mM KCl. Crystals soaked with 1 mM mersalyl overnight for phasing.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.0055 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: 1.0055 Å / Relative weight: 1
ReflectionResolution: 2.58→42.333 Å / Num. obs: 5168 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.172 / Χ2: 1 / Net I/σ(I): 16.5
Reflection shellResolution: 2.58→2.69 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.834 / Num. unique obs: 607 / CC1/2: 0.861 / Rpim(I) all: 0.331 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→42.333 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.45 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2424 282 5.49 %
Rwork0.2115 --
obs0.2131 5135 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→42.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 21 6 1228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041247
X-RAY DIFFRACTIONf_angle_d0.8041689
X-RAY DIFFRACTIONf_dihedral_angle_d12.474750
X-RAY DIFFRACTIONf_chiral_restr0.052189
X-RAY DIFFRACTIONf_plane_restr0.007213
LS refinement shellResolution: 2.5802→3.2506 Å
RfactorNum. reflection% reflection
Rfree0.2542 150 -
Rwork0.2107 2353 -
obs--100 %
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)
10.88760.24350.40420.14870.04210.78580.17280.0456-0.4902-0.19860.1711-0.33110.6174-0.02130.77510.15870.03440.14350.0704-0.00940.005414.162524.97172.8299
20.6494-0.39850.47590.4374-0.43490.46330.1433-0.3142-0.3155-0.1249-0.0022-0.07920.12970.24480.33870.1122-0.00990.08590.2839-0.03050.341621.422429.686373.3333
30.6839-0.01430.21360.14130.09840.1760.0611-0.2891-0.16620.0135-0.1994-0.0144-0.01070.3031-0.59140.11830.04340.01680.21350.06650.325617.224726.831279.0353
41.29060.23810.47640.3038-0.19360.4023-0.1052-0.1704-0.4584-0.39660.3315-0.10260.1728-0.10210.38890.12930.0181-0.04950.0678-0.03680.14130.812222.060275.7857
50.03780.0548-0.01980.0743-0.02860.007-0.044-0.1805-0.2137-0.4019-0.1195-0.20910.3580.16180.0020.67060.25780.02210.6949-0.00830.28629.293214.431749.4456
61.65361.21140.05760.90130.03720.00390.0413-0.16950.82230.01530.09390.1653-0.13420.31920.00030.27840.0710.01790.4557-0.0190.19472.603914.383262.2153
70.71290.925-0.09441.186-0.11660.00470.0039-0.2797-0.4062-0.0449-0.41070.10720.69940.5967-0.11230.70070.0413-0.04220.38220.04510.20652.93276.276557.868
85.5646-0.59112.49011.3245-0.95581.5306-0.4521-0.08770.94140.4822-0.01770.0387-0.1079-0.1658-0.71680.3564-0.0660.11210.3678-0.05030.07240.628816.730948.8236
92.0160.5041.09580.57081.21532.5622-0.371-0.0210.1899-0.4584-0.3824-0.12180.05420.0229-0.58390.5022-0.2148-0.01970.61090.10740.25274.22729.700646.0067
100.22550.0459-0.01660.2434-0.09130.03480.03370.62240.01080.0132-0.31980.1371-0.2320.4042-0.18540.6374-0.12460.04960.6075-0.03060.234711.401630.379355.1638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 34 )
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 80 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 23 )
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 33 )
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 61 )
9X-RAY DIFFRACTION9chain 'B' and (resid 62 through 72 )
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 82 )

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