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- PDB-7qlr: Receptor-binding protein of Clostridium difficile phage CDHS-1 -

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Basic information

Entry
Database: PDB / ID: 7qlr
TitleReceptor-binding protein of Clostridium difficile phage CDHS-1
ComponentsCDHS1_22 Putative tail fiber protein
KeywordsVIRAL PROTEIN / Receptor-binding protein Binding protein for Clostridium difficile
Function / homologyTail fiber protein
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.462 Å
AuthorsWallis, R. / Dowah, A. / Clokie, M.R.J.
Funding supportLibya, 1items
OrganizationGrant numberCountry
Other governmentLibya
CitationJournal: To Be Published
Title: The structurome of a Clostridium difficile phage and the remarkable accurate prediction of its novel phage receptor-binding protein
Authors: Dowah, A. / Wallis, R. / Clokie, M.R.J.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDHS1_22 Putative tail fiber protein
B: CDHS1_22 Putative tail fiber protein
C: CDHS1_22 Putative tail fiber protein
D: CDHS1_22 Putative tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,92012
Polymers276,7264
Non-polymers1948
Water6,612367
1
A: CDHS1_22 Putative tail fiber protein
hetero molecules

D: CDHS1_22 Putative tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,4606
Polymers138,3632
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area5730 Å2
ΔGint-77 kcal/mol
Surface area48420 Å2
MethodPISA
2
B: CDHS1_22 Putative tail fiber protein
hetero molecules

C: CDHS1_22 Putative tail fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,4606
Polymers138,3632
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_646-x+1,y-1/2,-z+3/21
Buried area5840 Å2
ΔGint-73 kcal/mol
Surface area47940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 178.206, 227.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 616 or resid 700 through 701))
21(chain B and (resid 15 through 616 or resid 700 through 701))
31chain C
41(chain D and (resid 15 through 616 or resid 700 through 701))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 15 through 616 or resid 700 through 701))A15 - 616
121(chain A and (resid 15 through 616 or resid 700 through 701))A700 - 701
211(chain B and (resid 15 through 616 or resid 700 through 701))B15 - 616
221(chain B and (resid 15 through 616 or resid 700 through 701))B700 - 701
311chain CC15 - 616
411(chain D and (resid 15 through 616 or resid 700 through 701))D15 - 616
421(chain D and (resid 15 through 616 or resid 700 through 701))D700 - 701

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Components

#1: Protein
CDHS1_22 Putative tail fiber protein


Mass: 69181.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J1J928
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.27 Å3/Da / Density % sol: 71.19 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: .1M HEPES pH 7, containing 0.05M ammonium acetate, 0.15M magnesium sulphate heptahydrate, 12% PEG smear medium, and 4% acetone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.462→113.81 Å / Num. obs: 117323 / % possible obs: 95.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 42.71 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.074 / Net I/σ(I): 7.7
Reflection shellResolution: 2.462→2.741 Å / Rmerge(I) obs: 1.772 / Num. unique obs: 6094 / CC1/2: 0.601 / Rpim(I) all: 0.498

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.462→102.64 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 5884 5.02 %
Rwork0.1952 111428 -
obs0.1964 117312 68.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.26 Å2 / Biso mean: 48.863 Å2 / Biso min: 21.9 Å2
Refinement stepCycle: final / Resolution: 2.462→102.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18731 0 8 367 19106
Biso mean--63.7 45.62 -
Num. residues----2411
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10865X-RAY DIFFRACTION7.674TORSIONAL
12B10865X-RAY DIFFRACTION7.674TORSIONAL
13C10865X-RAY DIFFRACTION7.674TORSIONAL
14D10865X-RAY DIFFRACTION7.674TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDRfactor Rfree error
2.462-2.480.467530.294552X-RAY DIFFRACTION0
2.48-2.510.329460.3047109X-RAY DIFFRACTION0
2.51-2.540.3505170.2958219X-RAY DIFFRACTION0
2.54-2.570.3983250.3076434X-RAY DIFFRACTION0
2.57-2.610.3395390.285722X-RAY DIFFRACTION0
2.61-2.640.2592560.3018988X-RAY DIFFRACTION0
2.64-2.680.3136680.2961319X-RAY DIFFRACTION0
2.68-2.720.3245780.2881590X-RAY DIFFRACTION0
2.72-2.760.37911090.28441911X-RAY DIFFRACTION0
2.76-2.810.27711430.28422378X-RAY DIFFRACTION0
2.81-2.860.32041310.27722926X-RAY DIFFRACTION0
2.86-2.910.33451800.26423429X-RAY DIFFRACTION0
2.91-2.970.30851980.26644052X-RAY DIFFRACTION0
2.97-3.030.27282400.2624647X-RAY DIFFRACTION0
3.03-3.090.2652530.24884929X-RAY DIFFRACTION0
3.09-3.160.27092730.23985265X-RAY DIFFRACTION0
3.16-3.240.25272780.23115398X-RAY DIFFRACTION0
3.24-3.330.2413110.22185349X-RAY DIFFRACTION0
3.33-3.430.23792920.21795402X-RAY DIFFRACTION0
3.43-3.540.23792930.20415406X-RAY DIFFRACTION0
3.54-3.670.22233110.19895386X-RAY DIFFRACTION0
3.67-3.810.20682750.18555436X-RAY DIFFRACTION0
3.81-3.990.21882870.17115432X-RAY DIFFRACTION0
3.99-4.20.17942840.16435406X-RAY DIFFRACTION0
4.2-4.460.17283330.15675416X-RAY DIFFRACTION0
4.46-4.80.18422730.14985487X-RAY DIFFRACTION0
4.8-5.290.18712840.16435483X-RAY DIFFRACTION0
5.29-6.050.20832530.19675542X-RAY DIFFRACTION0
6.05-7.620.20782760.19145568X-RAY DIFFRACTION0
7.62-102.640.18053150.16735747X-RAY DIFFRACTION0
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)
10.4897-0.40160.34710.1909-0.23130.5472-0.10610.17010.0871-0.0765-0.0011-0.0282-0.11980.13820.05030.3-0.0833-0.12140.35040.17240.4333-4.939236.3812134.1798
20.2244-0.3895-0.17920.87580.16970.234-0.0412-0.0141-0.0681-0.0162-0.06370.10980.08890.00760.09310.23350.0460.01020.36450.05740.288739.7228-26.7379145.5413
30.2394-0.5921-0.02080.36650.0530.23790.07850.23420.1247-0.039-0.14960.01350.00820.04230.02420.2427-0.01470.01160.3623-0.13790.458921.961162.2568177.7053
40.16860.1493-0.04350.4889-0.11380.54620.0092-0.05610.06860.1632-0.0957-0.0584-0.29130.1170.08670.3442-0.0139-0.11740.41020.0480.308356.710242.6508151.4637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 14 through 616)A14 - 616
2X-RAY DIFFRACTION2(chain 'B' and resid 14 through 616)B14 - 616
3X-RAY DIFFRACTION3(chain 'C' and resid 15 through 616)C15 - 616
4X-RAY DIFFRACTION4(chain 'D' and resid 14 through 616)D14 - 616

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