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- PDB-3hdf: Crystal structure of truncated endolysin R21 from phage 21 -

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Basic information

Entry
Database: PDB / ID: 3hdf
TitleCrystal structure of truncated endolysin R21 from phage 21
ComponentsLysozyme
KeywordsHYDROLASE / lysozyme-like / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Late protein
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / host cell plasma membrane / membrane
Similarity search - Function
SAR-endolysin-like / Lysozyme - #40 / Endolysin T4 type / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / SAR-endolysin
Similarity search - Component
Biological speciesEnterobacteria phage P21 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsSun, Q. / Sacchettini, J.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Regulation of a muralytic enzyme by dynamic membrane topology.
Authors: Sun, Q. / Kuty, G.F. / Arockiasamy, A. / Xu, M. / Young, R. / Sacchettini, J.C.
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,64918
Polymers31,4762
Non-polymers1,17316
Water5,585310
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3538
Polymers15,7381
Non-polymers6157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,29610
Polymers15,7381
Non-polymers5589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.190, 109.673, 45.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lysozyme / / Lysis protein / Muramidase / Endolysin


Mass: 15738.151 Da / Num. of mol.: 2 / Fragment: UNP residues 27-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P21 (virus) / Gene: R / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27359, lysozyme
#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO THE AUTHORS RESIDUES PHE 105 AND VAL 106 ARE CORRECT IN THE PDB FILE.

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Bis-Tris propane, 2.5M sodium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2008
Details: Si(111) Double Crystal Monochromator. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 35740 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.038 / Χ2: 1.14 / Net I/σ(I): 44.163
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.766.10.37234880.8561100
1.76-1.836.10.27535420.9151100
1.83-1.916.10.19435281.0321100
1.91-2.026.10.13335231.2171100
2.02-2.146.10.135471.3981100
2.14-2.316.10.06835421.2681100
2.31-2.546.20.0535721.0871100
2.54-2.916.10.04835931.4961100
2.91-3.666.10.0336201.2641100
3.66-505.80.0237850.851198.9

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→34.793 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.801 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.231 1820 5.1 %
Rwork0.2 33895 -
obs-35715 99.84 %
Solvent computationBsol: 63.425 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 86.53 Å2 / Biso mean: 28.309 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.423 Å20 Å2-0 Å2
2--0.344 Å2-0 Å2
3----4.821 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 76 310 2459
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6471
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.0491
X-RAY DIFFRACTIONf_dihedral_angle_d8.3691
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.0651
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.7-1.7080.247486X-RAY DIFFRACTION6894
1.708-1.7170.254485X-RAY DIFFRACTION6895
1.717-1.7260.251517X-RAY DIFFRACTION6896
1.726-1.7350.246497X-RAY DIFFRACTION6895
1.735-1.7440.228487X-RAY DIFFRACTION6895
1.744-1.7530.241475X-RAY DIFFRACTION6896
1.753-1.7630.228471X-RAY DIFFRACTION6895
1.763-1.7720.244503X-RAY DIFFRACTION6894
1.772-1.7820.227516X-RAY DIFFRACTION6896
1.782-1.7930.224484X-RAY DIFFRACTION6894
1.793-1.8030.243491X-RAY DIFFRACTION6896
1.803-1.8140.21484X-RAY DIFFRACTION6895
1.814-1.8250.225480X-RAY DIFFRACTION6893
1.825-1.8360.221497X-RAY DIFFRACTION6896
1.836-1.8470.204498X-RAY DIFFRACTION6896
1.847-1.8590.228476X-RAY DIFFRACTION6896
1.859-1.8710.223525X-RAY DIFFRACTION6895
1.871-1.8830.221498X-RAY DIFFRACTION6896
1.883-1.8960.222487X-RAY DIFFRACTION6895
1.896-1.9090.211477X-RAY DIFFRACTION6895
1.909-1.9230.207479X-RAY DIFFRACTION6894
1.923-1.9360.202485X-RAY DIFFRACTION6895
1.936-1.9510.202524X-RAY DIFFRACTION6894
1.951-1.9650.206484X-RAY DIFFRACTION6896
1.965-1.9810.19479X-RAY DIFFRACTION6894
1.981-1.9960.201495X-RAY DIFFRACTION6895
1.996-2.0120.195512X-RAY DIFFRACTION6895
2.012-2.0290.199465X-RAY DIFFRACTION6895
2.029-2.0460.19502X-RAY DIFFRACTION6894
2.046-2.0640.185491X-RAY DIFFRACTION6894
2.064-2.0820.195497X-RAY DIFFRACTION6895
2.082-2.1010.189468X-RAY DIFFRACTION6894
2.101-2.1210.2508X-RAY DIFFRACTION6896
2.121-2.1420.19497X-RAY DIFFRACTION6893
2.142-2.1630.2483X-RAY DIFFRACTION6895
2.163-2.1850.174490X-RAY DIFFRACTION6895
2.185-2.2090.181486X-RAY DIFFRACTION6894
2.209-2.2330.196501X-RAY DIFFRACTION6894
2.233-2.2580.186501X-RAY DIFFRACTION6896
2.258-2.2850.188497X-RAY DIFFRACTION6895
2.285-2.3130.183496X-RAY DIFFRACTION6896
2.313-2.3420.192484X-RAY DIFFRACTION6894
2.342-2.3730.192525X-RAY DIFFRACTION6895
2.373-2.4050.191488X-RAY DIFFRACTION6896
2.405-2.440.197494X-RAY DIFFRACTION6894
2.44-2.4760.187500X-RAY DIFFRACTION6895
2.476-2.5150.192504X-RAY DIFFRACTION6895
2.515-2.5560.2488X-RAY DIFFRACTION6896
2.556-2.60.196510X-RAY DIFFRACTION6895
2.6-2.6470.213508X-RAY DIFFRACTION6896
2.647-2.6980.197506X-RAY DIFFRACTION6896
2.698-2.7530.217483X-RAY DIFFRACTION6894
2.753-2.8130.213520X-RAY DIFFRACTION6893
2.813-2.8790.208476X-RAY DIFFRACTION6894
2.879-2.9510.192513X-RAY DIFFRACTION6896
2.951-3.030.199512X-RAY DIFFRACTION6895
3.03-3.1190.199500X-RAY DIFFRACTION6895
3.119-3.220.176510X-RAY DIFFRACTION6895
3.22-3.3350.193489X-RAY DIFFRACTION6894
3.335-3.4680.177535X-RAY DIFFRACTION6896
3.468-3.6260.165502X-RAY DIFFRACTION6896
3.626-3.8170.148516X-RAY DIFFRACTION6895
3.817-4.0560.155506X-RAY DIFFRACTION6893
4.056-4.3690.164509X-RAY DIFFRACTION6894
4.369-4.8070.186507X-RAY DIFFRACTION6893
4.807-5.50.194533X-RAY DIFFRACTION6896
5.5-6.9210.253541X-RAY DIFFRACTION6896
6.921-34.8010.253562X-RAY DIFFRACTION6891

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