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- PDB-6smk: Crystal structure of catalytic domain A109H mutant of prophage-en... -

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Basic information

Entry
Database: PDB / ID: 6smk
TitleCrystal structure of catalytic domain A109H mutant of prophage-encoded M23 protein EnpA from Enterococcus faecalis.
ComponentsPeptidase_M23 domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / M23 family / prophage protein / peptidoglycan hydrolase / zinc metallopeptidase
Function / homologyPeptidase M23 / Peptidase family M23 / Duplicated hybrid motif / carbohydrate transport / Peptidase_M23 domain-containing protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.997 Å
AuthorsMalecki, P.H. / Mitkowski, P. / Czapinska, H. / Sabala, I.
Funding support Poland, 1items
OrganizationGrant numberCountry
Foundation for Polish ScienceTEAM TECH/2016-3/19, POIR.04.04.00-00-3D8D/16-00 Poland
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Characterization of EnpA D,L-Endopeptidase from Enterococcus faecalis Prophage Provides Insights into Substrate Specificity of M23 Peptidases.
Authors: Malecki, P.H. / Mitkowski, P. / Jagielska, E. / Trochimiak, K. / Mesnage, S. / Sabala, I.
History
DepositionAug 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase_M23 domain-containing protein
B: Peptidase_M23 domain-containing protein
D: Peptidase_M23 domain-containing protein
C: Peptidase_M23 domain-containing protein
E: Peptidase_M23 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,57110
Polymers75,2445
Non-polymers3275
Water70339
1
A: Peptidase_M23 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1142
Polymers15,0491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidase_M23 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1142
Polymers15,0491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Peptidase_M23 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1142
Polymers15,0491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Peptidase_M23 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1142
Polymers15,0491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Peptidase_M23 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1142
Polymers15,0491
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.469, 136.469, 325.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Peptidase_M23 domain-containing protein


Mass: 15048.726 Da / Num. of mol.: 5 / Mutation: A109H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: EF_1473 / Production host: Escherichia coli (E. coli) / References: UniProt: Q835A4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 6.38 Å3/Da / Density % sol: 80.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.8M succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9116 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 2.997→49.246 Å / Num. obs: 36807 / % possible obs: 99.8 % / Redundancy: 21.806 % / Biso Wilson estimate: 83.129 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.211 / Rrim(I) all: 0.216 / Χ2: 1.117 / Net I/σ(I): 15.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.1822.5482.931.05130307582657790.4342.99799.2
3.18-3.422.3141.472.3121969546654660.7961.504100
3.4-3.6720.9360.6884.92107046511351130.9470.705100
3.67-4.0123.1670.3829.21110277476147600.9880.391100
4.01-4.4822.6380.18917.5496892428142800.9960.193100
4.48-5.1720.9090.11926.2880815386538650.9980.122100
5.17-6.3221.5630.10928.8970985329232920.9980.112100
6.32-8.8621.0330.06942.2455316263026300.9990.071100
8.86-49.24617.8940.03963.4329024163916220.9990.04199

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SLU

3slu


Resolution: 2.997→49.246 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.57
RfactorNum. reflection% reflection
Rfree0.2588 1841 5 %
Rwork0.2246 --
obs0.2263 36802 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 205.3 Å2 / Biso mean: 99.6079 Å2 / Biso min: 51.43 Å2
Refinement stepCycle: final / Resolution: 2.997→49.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 5 39 4883
Biso mean--85.83 80.79 -
Num. residues----646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.997-3.07760.41071360.4076258898
3.0776-3.16820.34311400.34642646100
3.1682-3.27040.35821380.30792620100
3.2704-3.38730.3451390.27432640100
3.3873-3.52290.26831390.25032652100
3.5229-3.68320.29051400.24442660100
3.6832-3.87730.27811400.22122658100
3.8773-4.12010.27611400.21322664100
4.1201-4.4380.2121410.18612670100
4.438-4.88420.24631430.17692714100
4.8842-5.59020.19821430.19452719100
5.5902-7.03970.26581460.21892775100
7.0397-49.2460.23921560.23192955100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.17881.72370.63856.874-0.92913.21-0.19630.1905-0.5222-0.5672-0.0936-0.5210.23340.33390.28890.7307-0.12610.18370.70540.08930.619911.2665-2.831342.3103
25.68671.00110.96436.32961.19025.36820.00170.09070.7163-0.6656-0.0152-0.3062-0.72410.26620.02580.7934-0.07710.08960.41390.07160.62812.628320.697928.0691
38.07960.37292.5546.67250.2322.7211-0.0589-0.40360.7597-0.1303-0.1599-0.1569-0.78720.51750.23821.0434-0.3380.11720.8053-0.11340.775336.414338.693242.7226
43.4508-0.98331.73215.8295-0.69425.4423-0.30750.0306-0.5702-0.5399-0.1515-0.19260.36680.06370.49561.0204-0.23680.23540.60050.05431.144354.930434.72118.578
56.94972.7902-1.31847.578-0.79225.10310.0362-0.6399-0.9834-0.2721-0.1644-0.45480.3834-0.00050.12410.7417-0.19630.08640.67880.20450.992140.585811.836137.7154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 131)A5 - 131
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 129)B3 - 129
3X-RAY DIFFRACTION3(chain 'D' and resid 3 through 129)D3 - 129
4X-RAY DIFFRACTION4(chain 'E' and resid 3 through 129)E3 - 129
5X-RAY DIFFRACTION5(chain 'C' and resid 3 through 129)C3 - 129

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