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- PDB-6o43: Crystal structure of a lysin protein from Staphylococcus phage P68 -

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Basic information

Entry
Database: PDB / ID: 6o43
TitleCrystal structure of a lysin protein from Staphylococcus phage P68
ComponentsOrf11
KeywordsANTIMICROBIAL PROTEIN / lysin / bacteriophage protein
Function / homologyCHAP domain / CHAP domain / Chem-I3C / Peptidase C51 domain-containing protein
Function and homology information
Biological speciesStaphylococcus phage P68 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08222992502 Å
AuthorsTruong, J.Q.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP150103009 Australia
Australian Research Council (ARC)DP160101450 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68.
Authors: Truong, J.Q. / Panjikar, S. / Shearwin-Whyatt, L. / Bruning, J.B. / Shearwin, K.E.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Refinement description
Category: citation / pdbx_refine_tls
Item: _citation.pdbx_database_id_DOI / _pdbx_refine_tls.pdbx_refine_id
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orf11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4862
Polymers21,9271
Non-polymers5591
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.397, 61.397, 101.606
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21A-520-

HOH

31A-521-

HOH

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Components

#1: Protein Orf11


Mass: 21926.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage P68 (virus) / Gene: Orf11 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q859J2
#2: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.51 % / Description: Cubic crystal
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.04 M Citric acid, 0.06 M BIS-TRIS propane / pH 6.4, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.459 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.08222992502→36.73 Å / Num. obs: 13689 / % possible obs: 98.3 % / Redundancy: 19.5 % / Biso Wilson estimate: 42.2454263453 Å2 / CC1/2: 1 / Rpim(I) all: 0.013 / Rrim(I) all: 0.06 / Net I/σ(I): 22.2
Reflection shellResolution: 2.08222992502→2.13 Å / Redundancy: 17.1 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 853 / CC1/2: 0.983 / Rpim(I) all: 0.134 / Rrim(I) all: 0.578 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIXdev_2689refinement
XDSdata reduction
Aimlessv0.7.2data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08222992502→36.73 Å / SU ML: 0.260477492419 / Cross valid method: FREE R-VALUE / σ(F): 1.90742038698 / Phase error: 28.0288712092
RfactorNum. reflection% reflection
Rfree0.224485331672 1639 6.63213693198 %
Rwork0.179222560999 --
obs0.182250142966 13297 96.3770376726 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.1674504078 Å2
Refinement stepCycle: LAST / Resolution: 2.08222992502→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 16 124 1659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002550177462941593
X-RAY DIFFRACTIONf_angle_d0.4834322083892171
X-RAY DIFFRACTIONf_chiral_restr0.0375788016022225
X-RAY DIFFRACTIONf_plane_restr0.00302147255904286
X-RAY DIFFRACTIONf_dihedral_angle_d9.63271916306914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0822-2.14350.2863460883351370.2514889251031745X-RAY DIFFRACTION89.4486692015
2.1435-2.21270.3441968309351180.2390344962062009X-RAY DIFFRACTION98.3811285846
2.2127-2.29170.2724224146621440.230394795911905X-RAY DIFFRACTION96.4689265537
2.2917-2.38350.3615755186591300.2252850110051911X-RAY DIFFRACTION95.4184198223
2.3835-2.49190.2747012963071270.2170819962241899X-RAY DIFFRACTION94.8946135831
2.4919-2.62330.299207059541420.2143378410911890X-RAY DIFFRACTION95.3990610329
2.6233-2.78760.2567951510031630.2085981524691916X-RAY DIFFRACTION96.3838664812
2.7876-3.00270.2830427761341260.2186423454311925X-RAY DIFFRACTION96.3363081259
3.0027-3.30470.2753882513351320.2197672139891977X-RAY DIFFRACTION98.5514018692
3.3047-3.78250.2190978097511400.1679781801431950X-RAY DIFFRACTION98.1681540629
3.7825-4.76390.1733440314751400.1301583440951995X-RAY DIFFRACTION99.2100371747
4.7639-36.73760.1622427454131400.1548476318911952X-RAY DIFFRACTION97.8027115475
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)
19.85838493609-7.065917294458.422585708736.36368179457-6.265689608289.39632971077-0.6460287183790.04367958840121.15800895433-0.0995112228615-0.097690412957-0.361918173697-0.5394460380140.2976233411890.589251615640.451169724674-0.135723042997-0.04804153072590.551163419633-0.03819320063420.3981032475643.7867500087534.782343803821.0284680052
22.473132009281.64669423279-0.9823058127612.40305945973-0.9910535719556.876410958290.0702071865880.0829628597902-0.06041266882270.07757871771270.16158647852-0.1877331349310.459300103550.444262286122-0.1829007890120.3495850265470.102924160139-0.04411721748190.472621597259-0.08784192558130.3307528521019.4740193154220.376551193138.3106739478
32.7062684145-0.4825523168111.693900397253.00249436199-0.1789779617444.79264476427-0.1710425774520.0149212221668-0.0847497816424-0.2280194329040.208232587618-0.2086653317151.00800776536-0.00430946414964-0.01112355380520.5225724517120.0197487982658-0.02073226778170.468953844262-0.1055676744520.51063617514.0425285451614.252946254627.5611514734
44.8857779466-1.654358667672.783276500091.65146603175-0.1778579463696.10128066875-0.07911239210230.401528118145-0.293808465489-0.1533530533320.33424369702-0.06530948755540.7194698595220.75332621349-0.277754087260.491696845657-0.04464534094160.03689555663340.61218996075-0.08806093775550.394588021884.5606993383920.101621749815.9494555202
55.813260643970.2646007349462.146127135672.972733054970.6354792996835.93976206457-0.0115986075629-0.01067933823990.0600770342523-0.2617555976750.138562321125-0.1173370110450.1319971954830.0346230821533-0.08517863004860.372499280268-0.115129528932-0.01833706604280.537058754375-0.02162944900180.317623911178-0.61289580636928.578407189816.6700234051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 96 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 207 )
4X-RAY DIFFRACTION4chain 'A' and (resid 9 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 95 )

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