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- PDB-1s2b: Structure of SCP-B the first member of the Eqolisin family of Pep... -

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Basic information

Entry
Database: PDB / ID: 1s2b
TitleStructure of SCP-B the first member of the Eqolisin family of Peptidases to have its structure determined
ComponentsScytalidopepsin B
KeywordsHYDROLASE / BETA SANDWICH / carboxyl peptidase / protease / proteinase / Eqolisin family
Function / homology
Function and homology information


scytalidopepsin B / glutamic-type endopeptidase activity / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Scytalidoglutamic peptidase / Peptidase G1 / Peptidase G1 / Peptidase G1 superfamily / Peptidase A4 family / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesScytalidium lignicola (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsFujinaga, M. / Cherney, M.M. / Oyama, H. / Oda, K. / James, M.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum
Authors: Fujinaga, M. / Cherney, M.M. / Oyama, H. / Oda, K. / James, M.N.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Scytalidopepsin B


Theoretical massNumber of molelcules
Total (without water)21,5541
Polymers21,5541
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.601, 108.601, 114.15
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

21A-214-

HOH

31A-215-

HOH

41A-291-

HOH

51A-341-

HOH

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Components

#1: Protein Scytalidopepsin B / Acid protease B / SLB


Mass: 21553.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scytalidium lignicola (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P15369, scytalidopepsin B
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.51 Å3/Da / Density % sol: 72.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 42% ammonium sulphate, 0.1M sodium acetate, 10% v/v ethelene glycol, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001
RadiationMonochromator: Beamline 9.1 SSRL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 18539 / % possible obs: 96.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.246 1032
Rwork0.23 -
obs-18539
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 0 167 1615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006

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