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- PDB-5udm: Phage-associated cell wall hydrolase PlyPy from Streptococcus pyo... -

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Basic information

Entry
Database: PDB / ID: 5udm
TitlePhage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes, space group P6522
ComponentsPhage-associated cell wall hydrolase
KeywordsHYDROLASE / lysin / d-alanyl-l-alanine endopeptidase / CHAP domain / Src Homology 3 domain superfamily / SH3 domain
Function / homologyBacterial SH3 domain / CHAP domain profile. / CHAP domain / CHAP domain / SH3-like domain, bacterial-type / Papain-like cysteine peptidase superfamily / hydrolase activity / : / Phage-associated cell wall hydrolase
Function and homology information
Biological speciesStreptococcus pyogenes MGAS5005 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsEdgar, R.J. / Korotkova, N. / Korotkov, K.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI113253 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: to be published
Title: Structure of phage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes
Authors: Edgar, R.J. / Korotkova, N. / Korotkov, K.V.
History
DepositionDec 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Phage-associated cell wall hydrolase
A: Phage-associated cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1466
Polymers57,7782
Non-polymers3684
Water1267
1
B: Phage-associated cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0733
Polymers28,8891
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Phage-associated cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0733
Polymers28,8891
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.970, 122.970, 163.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2:156 or resid 172:256))
21(chain B and (resid 2:17 or resid 25:109 or resid 129:256))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2:156 or resid 172:256))A2 - 156
121(chain A and (resid 2:156 or resid 172:256))A172 - 256
211(chain B and (resid 2:17 or resid 25:109 or resid 129:256))B2 - 17
221(chain B and (resid 2:17 or resid 25:109 or resid 129:256))B25 - 109
231(chain B and (resid 2:17 or resid 25:109 or resid 129:256))B129 - 256

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Components

#1: Protein Phage-associated cell wall hydrolase


Mass: 28888.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS5005 (bacteria)
Gene: M5005_Spy1001 / Plasmid: pET-21d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: A0A0C6FZU1, UniProt: J7M5V6*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M TRIS-HCL PH 7.0, 0.9M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2016 / Details: SI(111)
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.64→61.485 Å / Num. obs: 40496 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.236 % / Biso Wilson estimate: 54.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.101 / Χ2: 0.998 / Net I/σ(I): 11.69 / Num. measured all: 131043 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
2.64-2.713.090.9311.2329390.47798.3
2.71-2.783.2450.71.680.6499.8
2.78-2.863.2510.5352.180.75699.9
2.86-2.953.2470.4542.620.82199.8
2.95-3.053.2450.3263.630.88899.7
3.05-3.153.2650.2434.760.93899.9
3.15-3.273.240.1826.450.957100
3.27-3.413.2610.1318.930.98199.4
3.41-3.563.2490.10710.680.98799.6
3.56-3.733.2550.08213.380.99299.5
3.73-3.933.240.06715.930.99499.3
3.93-4.173.2460.05319.540.99699.3
4.17-4.463.2510.04622.690.99799.4
4.46-4.823.2430.03925.530.99799.3
4.82-5.283.2530.03725.690.99898.9
5.28-5.93.2580.03725.420.99899
5.9-6.813.2460.03924.220.99899.5
6.81-8.353.2280.03227.290.99999.4
8.35-11.83.2330.02433.410.99999.3
11.8-61.4853.1330.02332.390.99995.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEVERSION May 1, 2016 BUILT=20160617data scaling
PHASER2.7.12phasing
PHENIXdev_2481refinement
PDB_EXTRACT3.22data extraction
XDSVERSION May 1, 2016 BUILT=20160617data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.64→61.485 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1972 4.87 %RANDOM SELECTION
Rwork0.2101 ---
obs0.2114 40475 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.1 Å2 / Biso mean: 63.1222 Å2 / Biso min: 35.54 Å2
Refinement stepCycle: final / Resolution: 2.64→61.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 56 7 3450
Biso mean--73.63 49.04 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033497
X-RAY DIFFRACTIONf_angle_d0.5414759
X-RAY DIFFRACTIONf_chiral_restr0.046500
X-RAY DIFFRACTIONf_plane_restr0.004612
X-RAY DIFFRACTIONf_dihedral_angle_d13.4691960
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2437X-RAY DIFFRACTION7.561TORSIONAL
12B2437X-RAY DIFFRACTION7.561TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6392-2.70520.34921130.32982715282898
2.7052-2.77840.35111500.310227672917100
2.7784-2.86010.32811450.293127602905100
2.8601-2.95240.29321520.278727332885100
2.9524-3.0580.28281520.250227622914100
3.058-3.18040.32061570.238627432900100
3.1804-3.32510.26821130.243728052918100
3.3251-3.50040.27741270.23392765289299
3.5004-3.71970.27111400.210527622902100
3.7197-4.00690.22461380.20062741287999
4.0069-4.410.19311430.16462752289599
4.41-5.04790.19031430.15282734287799
5.0479-6.35870.18841670.17622713288099
6.3587-61.50170.19581320.20942751288398

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