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- PDB-6pym: Structure of active-site serine mutant of ESP, serine protease fr... -

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Basic information

Entry
Database: PDB / ID: 6pym
TitleStructure of active-site serine mutant of ESP, serine protease from Staphylococcus epidermidis
ComponentsGlutamyl endopeptidase
KeywordsHYDROLASE / serine protease
Function / homology
Function and homology information


glutamyl endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
: / Serine proteases, V8 family, serine active site / Serine proteases, V8 family, serine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan ...: / Serine proteases, V8 family, serine active site / Serine proteases, V8 family, serine active site. / Peptidase S1B, exfoliative toxin / Peptidase S1B / Trypsin-like peptidase domain / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Glutamyl endopeptidase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.20001815136 Å
AuthorsManne, K. / Narayana, S.V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01- AI106808 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2020
Title: Structural insights into the role of the N-terminus in the activation and function of extracellular serine protease from Staphylococcus epidermidis
Authors: Manne, K. / Narayana, S.V.L.
History
DepositionJul 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)23,5861
Polymers23,5861
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.621, 61.026, 42.512
Angle α, β, γ (deg.)90.000, 98.660, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glutamyl endopeptidase / Glutamic acid-specific protease / GluSE


Mass: 23586.098 Da / Num. of mol.: 1 / Mutation: S235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (strain ATCC 12228) (bacteria)
Strain: ATCC 12228 / Gene: gseA, esp, SE_1543 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0Q2, glutamyl endopeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→39.1692907212 Å / Num. obs: 119842 / % possible obs: 97 % / Redundancy: 2 % / Biso Wilson estimate: 9.77409682348 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.01531 / Rrim(I) all: 0.02166 / Net I/σ(I): 30.81
Reflection shellResolution: 1.2→1.243 Å / Redundancy: 2 % / Num. unique obs: 5576 / CC1/2: 0.995 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JCN

4jcn


Resolution: 1.20001815136→39.1692907212 Å / SU ML: 0.0690480134744 / Cross valid method: FREE R-VALUE / σ(F): 1.38629192932 / Phase error: 15.2982680205
RfactorNum. reflection% reflection
Rfree0.164619723987 3505 2.96430987821 %
Rwork0.158619642272 --
obs0.158801782518 118240 95.9966225816 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.2040010801 Å2
Refinement stepCycle: LAST / Resolution: 1.20001815136→39.1692907212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 0 299 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004474192625531683
X-RAY DIFFRACTIONf_angle_d0.8247278019032293
X-RAY DIFFRACTIONf_chiral_restr0.0911191660627250
X-RAY DIFFRACTIONf_plane_restr0.00551443515854310
X-RAY DIFFRACTIONf_dihedral_angle_d13.4756638682612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.20001815136-1.2430.1935610604451060.167718230663967X-RAY DIFFRACTION82.0012079726
1.2165-1.23380.1816590078451420.1721603446154267X-RAY DIFFRACTION90.0163331972
1.2338-1.25230.1820240027271540.1687304667734657X-RAY DIFFRACTION97.0938446014
1.2523-1.27180.1842131080551330.1636322877394711X-RAY DIFFRACTION98.4552845528
1.2718-1.29270.1659106235321410.1634564026194688X-RAY DIFFRACTION98.6315359477
1.2927-1.3150.1538284965931480.1552277892554674X-RAY DIFFRACTION98.3479502346
1.315-1.33890.1868222136771350.1599691383294700X-RAY DIFFRACTION98.1925264013
1.3389-1.36460.1534440057311440.1613711924774697X-RAY DIFFRACTION98.1748124113
1.3646-1.39250.1722668633451430.1531274659394646X-RAY DIFFRACTION97.8545157336
1.3925-1.42280.1640848975651600.1542950750624732X-RAY DIFFRACTION97.6252245061
1.4228-1.45590.1854426038311320.1537663594154668X-RAY DIFFRACTION97.1856651144
1.4559-1.49230.1287439404081430.1523019909464569X-RAY DIFFRACTION96.3599182004
1.4923-1.53260.1830094516171530.1549663328974727X-RAY DIFFRACTION99.0661794559
1.5326-1.57770.1750567817581490.1559403272324750X-RAY DIFFRACTION99.0097008892
1.5777-1.62870.1864539355821420.1583859881084679X-RAY DIFFRACTION98.8314883149
1.6287-1.68690.1933042047111410.1473982573034741X-RAY DIFFRACTION98.4869880976
1.6869-1.75440.1448759410611310.1527639684374696X-RAY DIFFRACTION98.5303123086
1.7544-1.83420.1760307422071580.1536080458184655X-RAY DIFFRACTION97.3109583502
1.8342-1.93090.1642359242981280.1529256124714631X-RAY DIFFRACTION96.6098254162
1.9309-2.05190.1355818875691370.1502230477544505X-RAY DIFFRACTION94.4455747711
2.0519-2.21030.134811951621500.1470103664554775X-RAY DIFFRACTION98.9353153877
2.2103-2.43270.1532636507461360.1596274672674692X-RAY DIFFRACTION98.9141569351
2.4327-2.78470.1903385361831490.1696378781714698X-RAY DIFFRACTION98.6164801628
2.7847-3.50810.1636888065331380.1546348148014560X-RAY DIFFRACTION95.1782820097
3.5081-39.16929072120.1637473264051120.1768054615313650X-RAY DIFFRACTION76.246453182

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