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- PDB-3hde: Crystal structure of full-length endolysin R21 from phage 21 -

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Basic information

Entry
Database: PDB / ID: 3hde
TitleCrystal structure of full-length 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 / cytolysis / defense response to bacterium / host cell plasma membrane / integral component of membrane
Similarity search - Function
SAR-endolysin-like / Lysozyme - #40 / Endolysin T4 type / Lysozyme domain superfamily / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P21 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.95 Å
AuthorsSun, Q. / Arockiasamy, A. / McKee, E. / Caronna, E. / 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: 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
C: Lysozyme
D: Lysozyme


Theoretical massNumber of molelcules
Total (without water)72,1604
Polymers72,1604
Non-polymers00
Water6,575365
1
A: Lysozyme
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)36,0802
Polymers36,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysozyme
D: Lysozyme


Theoretical massNumber of molelcules
Total (without water)36,0802
Polymers36,0802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)78.249, 94.814, 97.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18039.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P21 (bacteriophage)
Gene: R / Plasmid: pETR21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P27359, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 150mM Sodium acetate, 2M sodium formate, pH 4.6, 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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 53709 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.062 / Χ2: 1.21 / Net I/σ(I): 45.0787
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 4.0351 / Num. unique all: 1937 / Χ2: 0.849 / % possible all: 98.9

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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: 1.95→43.41 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.771 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.248 1552 3.06 %
Rwork0.212 --
obs-50721 94.6 %
Solvent computationBsol: 61.62 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 80.73 Å2 / Biso mean: 40.995 Å2 / Biso min: 21.71 Å2
Baniso -1Baniso -2Baniso -3
1--17.673 Å20 Å20 Å2
2--9.626 Å20 Å2
3---8.047 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 0 365 5281
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.70
X-RAY DIFFRACTIONf_bond_d0.0050
X-RAY DIFFRACTIONf_chiral_restr0.0530
X-RAY DIFFRACTIONf_dihedral_angle_d9.9770
X-RAY DIFFRACTIONf_plane_restr0.0030
X-RAY DIFFRACTIONf_nbd_refined4.0560
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.95-1.9570.266425X-RAY DIFFRACTION9874
1.957-1.9640.267410X-RAY DIFFRACTION9879
1.964-1.970.295389X-RAY DIFFRACTION9874
1.97-1.9770.263407X-RAY DIFFRACTION9877
1.977-1.9840.261449X-RAY DIFFRACTION9880
1.984-1.9920.254435X-RAY DIFFRACTION9881
1.992-1.9990.259427X-RAY DIFFRACTION9880
1.999-2.0060.23448X-RAY DIFFRACTION9880
2.006-2.0140.261446X-RAY DIFFRACTION9883
2.014-2.0210.259433X-RAY DIFFRACTION9883
2.021-2.0290.245461X-RAY DIFFRACTION9884
2.029-2.0370.271433X-RAY DIFFRACTION9880
2.037-2.0450.233449X-RAY DIFFRACTION9884
2.045-2.0530.237469X-RAY DIFFRACTION9886
2.053-2.0610.249483X-RAY DIFFRACTION9889
2.061-2.0690.228466X-RAY DIFFRACTION9888
2.069-2.0780.243462X-RAY DIFFRACTION9886
2.078-2.0860.229459X-RAY DIFFRACTION9887
2.086-2.0950.231482X-RAY DIFFRACTION9887
2.095-2.1040.221466X-RAY DIFFRACTION9885
2.104-2.1130.22458X-RAY DIFFRACTION9888
2.113-2.1220.238508X-RAY DIFFRACTION9888
2.122-2.1320.227443X-RAY DIFFRACTION9888
2.132-2.1410.234476X-RAY DIFFRACTION9889
2.141-2.1510.237501X-RAY DIFFRACTION9888
2.151-2.1610.231486X-RAY DIFFRACTION9889
2.161-2.1710.246470X-RAY DIFFRACTION9889
2.171-2.1810.241487X-RAY DIFFRACTION9891
2.181-2.1920.226482X-RAY DIFFRACTION9889
2.192-2.2030.237478X-RAY DIFFRACTION9888
2.203-2.2140.235485X-RAY DIFFRACTION9890
2.214-2.2250.243503X-RAY DIFFRACTION9893
2.225-2.2360.222499X-RAY DIFFRACTION9890
2.236-2.2480.215487X-RAY DIFFRACTION9892
2.248-2.2590.236475X-RAY DIFFRACTION9890
2.259-2.2720.225501X-RAY DIFFRACTION9889
2.272-2.2840.24494X-RAY DIFFRACTION9893
2.284-2.2960.225486X-RAY DIFFRACTION9892
2.296-2.3090.231530X-RAY DIFFRACTION9892
2.309-2.3220.216489X-RAY DIFFRACTION9893
2.322-2.3360.23489X-RAY DIFFRACTION9891
2.336-2.350.221484X-RAY DIFFRACTION9892
2.35-2.3640.213536X-RAY DIFFRACTION9894
2.364-2.3780.227495X-RAY DIFFRACTION9893
2.378-2.3930.228506X-RAY DIFFRACTION9895
2.393-2.4090.231508X-RAY DIFFRACTION9891
2.409-2.4240.23509X-RAY DIFFRACTION9893
2.424-2.440.238520X-RAY DIFFRACTION9893
2.44-2.4570.24499X-RAY DIFFRACTION9894
2.457-2.4740.237496X-RAY DIFFRACTION9894
2.474-2.4910.223509X-RAY DIFFRACTION9894
2.491-2.5090.225514X-RAY DIFFRACTION9891
2.509-2.5270.217516X-RAY DIFFRACTION9896
2.527-2.5460.234505X-RAY DIFFRACTION9895
2.546-2.5660.219542X-RAY DIFFRACTION9895
2.566-2.5860.219484X-RAY DIFFRACTION9895
2.586-2.6070.23530X-RAY DIFFRACTION9895
2.607-2.6290.237518X-RAY DIFFRACTION9895
2.629-2.6510.233509X-RAY DIFFRACTION9895
2.651-2.6740.236529X-RAY DIFFRACTION9895
2.674-2.6980.23532X-RAY DIFFRACTION9897
2.698-2.7230.214527X-RAY DIFFRACTION9896
2.723-2.7480.24503X-RAY DIFFRACTION9895
2.748-2.7750.228526X-RAY DIFFRACTION9895
2.775-2.8030.236540X-RAY DIFFRACTION9895
2.803-2.8320.226489X-RAY DIFFRACTION9896
2.832-2.8620.231531X-RAY DIFFRACTION9896
2.862-2.8930.234540X-RAY DIFFRACTION9896
2.893-2.9260.221517X-RAY DIFFRACTION9896
2.926-2.9610.212537X-RAY DIFFRACTION9896
2.961-2.9970.211512X-RAY DIFFRACTION9896
2.997-3.0340.226526X-RAY DIFFRACTION9897
3.034-3.0740.229540X-RAY DIFFRACTION9896
3.074-3.1160.217521X-RAY DIFFRACTION9897
3.116-3.1610.235539X-RAY DIFFRACTION9896
3.161-3.2080.225518X-RAY DIFFRACTION9897
3.208-3.2580.214548X-RAY DIFFRACTION9897
3.258-3.3120.221522X-RAY DIFFRACTION9897
3.312-3.3690.208517X-RAY DIFFRACTION9895
3.369-3.430.21543X-RAY DIFFRACTION9897
3.43-3.4960.221545X-RAY DIFFRACTION9896
3.496-3.5670.205529X-RAY DIFFRACTION9896
3.567-3.6450.182533X-RAY DIFFRACTION9897
3.645-3.730.187546X-RAY DIFFRACTION9897
3.73-3.8230.172523X-RAY DIFFRACTION9896
3.823-3.9260.183544X-RAY DIFFRACTION9896
3.926-4.0420.186530X-RAY DIFFRACTION9897
4.042-4.1720.173538X-RAY DIFFRACTION9897
4.172-4.3210.184546X-RAY DIFFRACTION9897
4.321-4.4940.2541X-RAY DIFFRACTION9897
4.494-4.6980.169541X-RAY DIFFRACTION9897
4.698-4.9450.191549X-RAY DIFFRACTION9897
4.945-5.2550.182548X-RAY DIFFRACTION9897
5.255-5.660.204551X-RAY DIFFRACTION9897
5.66-6.2280.205549X-RAY DIFFRACTION9897
6.228-7.1250.205565X-RAY DIFFRACTION9897
7.125-8.9640.178566X-RAY DIFFRACTION9897
8.964-43.4180.188562X-RAY DIFFRACTION9889

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