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- PDB-9ms7: Crystal structure of a putative phage endolysin identified from a... -

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Basic information

Entry
Database: PDB / ID: 9ms7
TitleCrystal structure of a putative phage endolysin identified from a metagenomic survey of Prosser, Washington soil (PWe2)
ComponentsPWe2 endolysin
KeywordsHYDROLASE / endolysin / carbohydrate-metabolizing / soil phage enzyme
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Assembly

Deposited unit
A: PWe2 endolysin
B: PWe2 endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8689
Polymers41,5732
Non-polymers2957
Water3,675204
1
A: PWe2 endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9595
Polymers20,7871
Non-polymers1734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PWe2 endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9084
Polymers20,7871
Non-polymers1223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.046, 34.738, 110.760
Angle α, β, γ (deg.)90.00, 107.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PWe2 endolysin


Mass: 20786.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES: NaOH, pH 7.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→36.8 Å / Num. obs: 53615 / % possible obs: 99.1 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Net I/σ(I): 16.2
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2564 / CC1/2: 0.7 / Rpim(I) all: 0.46

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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: 1.5→36.8 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1924 2652 4.95 %
Rwork0.1512 --
obs0.1532 53581 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 16 204 3110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053001
X-RAY DIFFRACTIONf_angle_d0.7394048
X-RAY DIFFRACTIONf_dihedral_angle_d17.0251149
X-RAY DIFFRACTIONf_chiral_restr0.048431
X-RAY DIFFRACTIONf_plane_restr0.008530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.35671450.29992601X-RAY DIFFRACTION99
1.53-1.560.29871300.23272660X-RAY DIFFRACTION99
1.56-1.590.29361440.20172734X-RAY DIFFRACTION99
1.59-1.620.24761380.17832587X-RAY DIFFRACTION99
1.62-1.660.26321210.15272722X-RAY DIFFRACTION99
1.66-1.70.21471330.14572652X-RAY DIFFRACTION99
1.7-1.750.21491550.13192629X-RAY DIFFRACTION98
1.75-1.80.18451310.12752591X-RAY DIFFRACTION98
1.8-1.860.21221530.13892691X-RAY DIFFRACTION100
1.86-1.920.21981520.14772702X-RAY DIFFRACTION100
1.92-20.18451430.12732684X-RAY DIFFRACTION100
2-2.090.19971360.12152691X-RAY DIFFRACTION100
2.09-2.20.20231260.12722684X-RAY DIFFRACTION99
2.2-2.340.1641470.13022686X-RAY DIFFRACTION99
2.34-2.520.15811340.14622631X-RAY DIFFRACTION97
2.52-2.770.19591250.15382725X-RAY DIFFRACTION100
2.78-3.180.21771460.16632738X-RAY DIFFRACTION100
3.18-40.1811420.14612740X-RAY DIFFRACTION100
4-36.80.15551510.16012781X-RAY DIFFRACTION98

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