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- PDB-6hlk: Hijacking the Hijackers: Escherichia coli Pathogenicity Islands R... -

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Basic information

Entry
Database: PDB / ID: 6hlk
TitleHijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit.
ComponentsRedirecting phage packaging protein C (RppC)
KeywordsDNA BINDING PROTEIN / Redirecting packaging protein / Homo-dimer / phage interference
Function / homologyPutative DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Redirecting phage packaging protein C (RppC)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.42 Å
AuthorsPenades, J.R. / Bacarizo, J. / Marina, A. / Alqasmi, M. / Fillol-Salom, A. / Roszak, A.W. / Ciges-Tomas, J.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council670932 United Kingdom
Citation
Journal: Mol.Cell / Year: 2019
Title: Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit.
Authors: Fillol-Salom, A. / Bacarizo, J. / Alqasmi, M. / Ciges-Tomas, J.R. / Martinez-Rubio, R. / Roszak, A.W. / Cogdell, R.J. / Chen, J. / Marina, A. / Penades, J.R.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Redirecting phage packaging protein C (RppC)


Theoretical massNumber of molelcules
Total (without water)18,0631
Polymers18,0631
Non-polymers00
Water00
1
A: Redirecting phage packaging protein C (RppC)

A: Redirecting phage packaging protein C (RppC)


Theoretical massNumber of molelcules
Total (without water)36,1262
Polymers36,1262
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1940 Å2
ΔGint-13 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.881, 56.881, 132.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Redirecting phage packaging protein C (RppC)


Mass: 18062.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein comes from Escherichia coli genome assembly 1.EC2733.1, contig U59_10. The protein was not described previously.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CXXR01000010.1 / Variant: EC2733.1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5H1ZR32*PLUS

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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: 3.5 Å3/Da / Density % sol: 64.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 15% PEG 8000, 0.1M Sodium Acetate pH6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4158→43.1316 Å / Num. obs: 7721 / % possible obs: 89.7 % / Redundancy: 6 % / Biso Wilson estimate: 69.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.033 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4158→7.375 Å

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Processing

Software
NameVersionClassification
AutoPROC1.0.5data collection
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
BUCCANEERCCP4 7.0.062model building
AutoSol1.13_2998phasing
RefinementMethod to determine structure: SAD / Resolution: 2.42→43.12 Å / SU ML: 0.308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9066
RfactorNum. reflection% reflection
Rfree0.2671 348 4.53 %
Rwork0.2374 --
obs0.2388 7686 86.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.3 Å2
Refinement stepCycle: LAST / Resolution: 2.42→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 0 0 1060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031080
X-RAY DIFFRACTIONf_angle_d0.67881443
X-RAY DIFFRACTIONf_chiral_restr0.0389146
X-RAY DIFFRACTIONf_plane_restr0.0027189
X-RAY DIFFRACTIONf_dihedral_angle_d2.8909652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-3.040.31131460.27923250X-RAY DIFFRACTION78.48
3.04-43.130.25942020.234088X-RAY DIFFRACTION93.85
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)
12.771359125042.495458246380.5897822042252.560703216430.9937915705410.867695731180.197926808436-0.238442817455-0.255597105857-0.59199210558-0.0701314954952-0.7259303110560.229386088019-0.201111026761-0.2345041207220.576161988321-0.05684473290320.06431792195590.6909628770670.1060648848310.57081893970918.293667144313.023650643913.6725297885
24.67524480933-4.485878420342.158196320665.92785719747-4.139539925123.67178262013-0.288081138403-1.8245809607-1.204749660371.83732101176-0.8096678668210.395922071882-1.76334692741-0.09693724364580.09592652646520.589730371259-0.0847445279659-0.1776111625810.8931114386220.02733745431990.67508062903316.85433751859.6235246253623.0141481764
35.7531545673-3.618402067080.4185805473643.65207610227-0.4272413580461.39355298744-0.6129204351071.08311457825-1.969990883861.30865676977-0.3690315681370.003511914067020.647837650662.886234892030.1244050331851.092800688680.298075386010.1919897322621.547608714670.3724096288240.80836618451226.1183208953.6438323630517.3756234
46.07801017772-2.14919276321-5.095681640353.305618283090.8015171858495.09200058852-0.2597579959290.4930085203890.296923489742-0.303771461769-0.0344254950566-0.0860670088777-0.2695780861880.0482579979910.2790878626790.489957533886-0.04433170158220.01993200548930.6074477660470.1303450176560.4809950199534.776455586767.4143599516822.8162543088
55.31031740683-6.205651495634.57289813127.26217776562-5.373659122293.970541134380.01166792467280.359630738442-0.150643329996-1.68723427711-1.473892854450.1357274226790.9205093780021.357165538990.9851629881922.98523606647-1.150666655570.360296999881.68145702644-0.2613163778491.34591223616-3.60112235936-9.3357889766915.3059932877
63.44217796571-1.80420216314-2.008187743.4664456196-3.48085108099.048274444150.01491411558770.269858308507-1.49111148198-0.0883825379545-0.491354482281-0.9877419839872.237702124850.3042595918230.5552442406130.6910319239170.2469825481790.2646722072040.568528792170.2417613808181.1593645384310.9999908572-6.0106146049322.3058514587
75.72252362273-1.38185596948-4.381228861053.30769906522-0.3003647246191.976555428380.3111273016010.833189133412-0.903867758816-0.339649662417-0.5615087796650.112717065664-0.1563492850060.2122196187180.3096458674940.4996909326730.01343073184940.05442843963170.5499945666660.05233005481650.464741940417-5.799050366373.1566840922931.1565671358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 121 )
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 137 )
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 165 )

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