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

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Basic information

Entry
Database: PDB / ID: 5udn
TitlePhage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes, space group P3121
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 / SH3-like domain, bacterial-type / CHAP domain profile. / CHAP domain / CHAP domain / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.971 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
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)57,6776
Polymers57,3092
Non-polymers3684
Water6,449358
1
B: Phage-associated cell wall hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8383
Polymers28,6541
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)28,8383
Polymers28,6541
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.130, 122.130, 89.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
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 129:156 or resid 172:256))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP(chain A and (resid 2:156 or resid 172:256))AB2 - 1561 - 155
12ARGARGGLUGLU(chain A and (resid 2:156 or resid 172:256))AB172 - 256171 - 255
21ALAALATHRTHR(chain B and (resid 2:17 or resid 25:109 or resid 129:156 or resid 172:256))BA2 - 171 - 16
22LEULEUGLNGLN(chain B and (resid 2:17 or resid 25:109 or resid 129:156 or resid 172:256))BA25 - 10924 - 108
23GLYGLYASPASP(chain B and (resid 2:17 or resid 25:109 or resid 129:156 or resid 172:256))BA129 - 156128 - 155
24ARGARGGLUGLU(chain B and (resid 2:17 or resid 25:109 or resid 129:156 or resid 172:256))BA172 - 256171 - 255

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Components

#1: Protein Phage-associated cell wall hydrolase


Mass: 28654.287 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.: 358 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M acetate PH 4.5, 1.0M ammonium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2016 / Details: Si(220)
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.97→68.291 Å / Num. obs: 54321 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.52 % / Biso Wilson estimate: 26.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsCC1/2% possible all
1.97-2.025.5631.111.6439760.60699.8
2.02-2.085.490.8172.330.7999.9
2.08-2.145.5720.7742.390.79499.9
2.14-2.25.5970.573.180.84599.9
2.2-2.285.3360.4784.060.92295.1
2.28-2.365.5970.424.270.89999.9
2.36-2.445.6140.3515.110.934100
2.44-2.545.6070.2965.980.953100
2.54-2.665.6030.2277.70.969100
2.66-2.795.540.1779.80.9899.9
2.79-2.945.6060.13112.780.989100
2.94-3.125.5750.09916.680.994100
3.12-3.335.5750.07122.360.997100
3.33-3.65.4780.05628.240.99899.8
3.6-3.945.2860.04733.160.99899
3.94-4.415.4280.03640.480.99999.9
4.41-5.095.3080.03143.970.99999.8
5.09-6.235.4350.03240.250.99999.8
6.23-8.815.4540.0341.850.999100
8.81-68.2915.1080.0256.730.99999.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.38 Å68.29 Å
Translation6.38 Å68.29 Å

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Processing

Software
NameVersionClassification
XSCALEVERSION May 1, 2016 BUILT=20160617data scaling
PHASER2.7.17phasing
PHENIXdev_2481refinement
PDB_EXTRACT3.22data extraction
XDSVERSION May 1, 2016 BUILT=20160617data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UDM

5udm


Resolution: 1.971→68.291 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 5079 4.88 %RANDOM SELECTION
Rwork0.2 ---
obs0.2012 54308 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.9 Å2 / Biso mean: 34.2854 Å2 / Biso min: 17.61 Å2
Refinement stepCycle: final / Resolution: 1.971→68.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 56 358 3816
Biso mean--36.37 34.57 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063513
X-RAY DIFFRACTIONf_angle_d0.7784780
X-RAY DIFFRACTIONf_chiral_restr0.056501
X-RAY DIFFRACTIONf_plane_restr0.006615
X-RAY DIFFRACTIONf_dihedral_angle_d13.8181966
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2514X-RAY DIFFRACTION7.768TORSIONAL
12B2514X-RAY DIFFRACTION7.768TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.971-1.99340.30121900.31373262345299
1.9934-2.01690.32541570.3133553512100
2.0169-2.04150.32131380.286133513489100
2.0415-2.06730.35081420.30913320346299
2.0673-2.09450.3841860.34233214340097
2.0945-2.12320.29421720.264733713543100
2.1232-2.15350.29242030.255132653468100
2.1535-2.18570.24991980.239533603558100
2.1857-2.21990.26741430.238733023445100
2.2199-2.25620.40561560.40523060321691
2.2562-2.29520.36871360.32283193332994
2.2952-2.33690.22071880.216332363424100
2.3369-2.38180.24272040.21633213525100
2.3818-2.43050.22052050.201233183523100
2.4305-2.48330.2431540.209733403494100
2.4833-2.54110.2561670.20083310347799
2.5411-2.60460.24861700.200133573527100
2.6046-2.67510.25641830.23270345399
2.6751-2.75380.22941650.19233361352699
2.7538-2.84270.18351720.180833143486100
2.8427-2.94430.22981870.191332843471100
2.9443-3.06210.20531880.183833253513100
3.0621-3.20150.22041230.179833913514100
3.2015-3.37030.21031510.174233613512100
3.3703-3.58140.22281510.17173331348299
3.5814-3.85790.17152170.17653197341498
3.8579-4.24610.16071800.14663287346798
4.2461-4.86040.13551320.13663322345499
4.8604-6.1230.18051500.15433318346899
6.123-68.33160.22921710.21593340351199

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