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- PDB-6q12: Structure of pro-Esp mutant- S66V -

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Basic information

Entry
Database: PDB / ID: 6q12
TitleStructure of pro-Esp mutant- S66V
ComponentsGlutamyl endopeptidaseGlutamyl endopeptidase GluV8
KeywordsHYDROLASE / serine protease / zymogen
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Glutamyl endopeptidase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 D Struct Biol / 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
DepositionAug 2, 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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 22, 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_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Oct 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
B: Glutamyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)55,2972
Polymers55,2972
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.650, 61.110, 75.470
Angle α, β, γ (deg.)90.000, 94.700, 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 / Glutamyl endopeptidase GluV8 / Glutamic acid-specific protease / GluSE


Mass: 27648.512 Da / Num. of mol.: 2 / Mutation: S66V
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 / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 1.77 Å3/Da / Density % sol: 30.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.225 M Ammonium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→42.51 Å / Num. obs: 18892 / % possible obs: 95 % / Redundancy: 1.5 % / Biso Wilson estimate: 11.8350592685 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.057 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.088 / Num. unique obs: 1779 / CC1/2: 0.966 / Rrim(I) all: 0.125

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PYM

6pym


Resolution: 2.2→42.51 Å / SU ML: 0.2585 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.34
RfactorNum. reflection% reflection
Rfree0.2336 980 5.19 %
Rwork0.173 --
obs0.1762 18888 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 10.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 0 275 3420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00653673482093214
X-RAY DIFFRACTIONf_angle_d0.7868736618874369
X-RAY DIFFRACTIONf_chiral_restr0.057515039913471
X-RAY DIFFRACTIONf_plane_restr0.00509510565304589
X-RAY DIFFRACTIONf_dihedral_angle_d11.83072347471887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.3150.27161570.1802240991.773962804
2.315-2.460.25831230.1804250093.2125088842
2.46-2.64990.26141230.18253293.816254417
2.6499-2.91650.26151370.1937252895.0427960057
2.9165-3.33840.24681470.1775254595.1236749117
3.3384-4.20540.18911430.152265698.0385288967
4.20540.21411500.1694273899.8962296783

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