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- PDB-9ms6: Crystal structure of a putative phage endolysin identified from a... -

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Basic information

Entry
Database: PDB / ID: 9ms6
TitleCrystal structure of a putative phage endolysin identified from a metagenomic survey of Prosser, Washington soil (PWe1)
ComponentsPWe1 endolysin
KeywordsHYDROLASE / endolysin / carbohydrate-metabolizing / soil phage enzyme
Function / homologyBROMIDE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSmith, C.A. / Buchko, G.W. / Wu, R. / Cort, J.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of two phage endolysins identified from a metagenomic survey of south-central Washington soil
Authors: Buchko, G.W. / Smith, C.A. / Wu, R. / Alfaro, T.D. / McClure, R.S. / Cort, J.R. / Hofmockel, K.F.
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PWe1 endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9814
Polymers23,7251
Non-polymers2563
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.842, 64.842, 85.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

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Components

#1: Protein PWe1 endolysin


Mass: 23724.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes, sodium pH 7.5, 2% v/v PEG 400, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91966 Å / Relative weight: 1
ReflectionResolution: 2.15→34.03 Å / Num. obs: 11764 / % possible obs: 99.9 % / Redundancy: 39 % / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.092 / Net I/σ(I): 27.9
Reflection shellResolution: 2.15→2.22 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 971 / CC1/2: 0.725 / Rpim(I) all: 0.531

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→34.03 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 616 5.26 %
Rwork0.2119 --
obs0.2147 11720 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 7 22 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081520
X-RAY DIFFRACTIONf_angle_d0.9742052
X-RAY DIFFRACTIONf_dihedral_angle_d19.41579
X-RAY DIFFRACTIONf_chiral_restr0.049217
X-RAY DIFFRACTIONf_plane_restr0.011272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.370.3081770.29822680X-RAY DIFFRACTION100
2.37-2.710.30781660.22992726X-RAY DIFFRACTION100
2.71-3.410.33041410.28142787X-RAY DIFFRACTION100
3.42-34.030.2371320.17852911X-RAY DIFFRACTION100
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)
11.74361.18453.72556.40972.66957.8859-0.26621.0507-0.2703-0.7880.8367-3.27341.17964.35810.65250.95410.86440.00881.40310.29450.6386-4.78231.5907-3.3363
20.2941-0.26140.14851.25690.7080.72370.11430.1773-0.14510.8519-0.3928-0.48260.98580.89230.0090.61590.24330.10690.83280.12760.6177-12.7116.45142.6248
30.8517-0.57360.61071.120.21980.68340.08390.3446-0.517-0.3963-0.1954-0.01191.8480.0297-0.00081.01040.17550.10420.6470.00240.7496-17.7289-1.1073-4.4054
40.76520.07930.03320.1319-0.39410.6720.0490.41550.0276-0.5079-0.67720.36072.22591.2146-0.00480.62970.18720.04410.78450.01890.7317-11.712212.2236-17.4804
50.48960.4351-0.24190.3784-0.21110.4677-1.080.8072-1.1981-1.554-0.0120.86451.07620.6155-0.00231.0383-0.0359-0.10710.7929-0.18321.1295-21.534812.2382-32.623
60.12710.1210.23790.12430.29940.5146-0.03392.6602-0.7914-1.29580.4615-0.0686-0.16761.1758-0.00730.7432-0.1993-0.01631.1317-0.22770.6904-17.976120.7859-33.8122
71.8296-1.4908-1.84081.10920.97282.03080.20540.0695-0.2005-0.1608-0.17620.33810.1192-0.16050.0010.3958-0.0203-0.0740.4260.00420.556-23.693420.1594-18.5811
81.3091-0.6436-0.22521.2695-1.11562.658-0.0054-0.29310.09120.23080.02780.0423-0.4544-0.1676-0.0010.4775-0.0529-0.01440.44950.03420.544-24.165719.9397-5.1815
90.9144-0.538-0.76991.2266-0.81792.02750.12970.1846-0.6513-0.0276-0.0139-0.23341.08170.203-0.00180.76910.03060.08850.6080.0510.6112-26.70983.7541-4.8691
100.20190.34920.20410.41070.45370.2874-1.2276-0.7433-0.0299-0.28060.70630.0491.2344-0.1769-0.01511.49090.25380.0280.955-0.05791.0474-12.3775-6.2892-11.9732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 29 )
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 48 )
4X-RAY DIFFRACTION4chain 'A' and (resid 49 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 86 )
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 122 )
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 171 )
10X-RAY DIFFRACTION10chain 'A' and (resid 172 through 206 )

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