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- PDB-4jcn: Structure of ESP, serine protease from Staphylococcus epidermidis -

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Basic information

Entry
Database: PDB / ID: 4jcn
TitleStructure of ESP, serine protease from Staphylococcus epidermidis
ComponentsGlutamyl endopeptidase
KeywordsHYDROLASE / extracellular serine protease / esp / biofilm / Glutamyl endopeptidase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKrishnan, V. / Sthanam, V.L.N.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Secreted proteases control autolysin-mediated biofilm growth of Staphylococcus aureus
Authors: Chen, C. / Krishnan, V. / Macon, K. / Manne, K. / Narayana, S.V. / Schneewind, O.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Glutamyl endopeptidase


Theoretical massNumber of molelcules
Total (without water)23,6021
Polymers23,6021
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.410, 60.360, 42.340
Angle α, β, γ (deg.)90.00, 98.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23602.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: JK16 / ATCC 12228 / Gene: esp, gseA, 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.: 185 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→41.87 Å / Num. obs: 17810 / % possible obs: 97.4 % / Redundancy: 5.16 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.14 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 5.9 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QY6

1qy6


Resolution: 1.8→41.86 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.633 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19859 901 5.1 %RANDOM
Rwork0.17335 ---
obs0.17473 16890 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.386 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.46 Å2
2--0.27 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 185 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191705
X-RAY DIFFRACTIONr_bond_other_d0.0010.021581
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9332324
X-RAY DIFFRACTIONr_angle_other_deg0.98633630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0245215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47525.69886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69415263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.34156
X-RAY DIFFRACTIONr_chiral_restr0.1330.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 68 -
Rwork0.369 1210 -
obs--94.95 %

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