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- PDB-1s2k: Structure of SCP-B a member of the Eqolisin family of Peptidases ... -

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Basic information

Entry
Database: PDB / ID: 1s2k
TitleStructure of SCP-B a member of the Eqolisin family of Peptidases in a complex with a Tripeptide Ala-Ile-His
Components
  • Ala-Ile-His tripeptide
  • Scytalidopepsin B
KeywordsHYDROLASE / Beta Sandwich / Pepstatin insensitive carboxyl peptidase / protease / proteinase / Eqolisin family / complex with Ala-Ile-His
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
TYROSINE / Scytalidopepsin B
Similarity search - Component
Biological speciesScytalidium lignicola (fungus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 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 11, 2017Group: Refinement description / Category: software
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scytalidopepsin B
B: Ala-Ile-His tripeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0753
Polymers21,8942
Non-polymers1811
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-2 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.369, 109.369, 113.829
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-1062-

HOH

21A-1073-

HOH

31A-1074-

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: Protein/peptide Ala-Ile-His tripeptide


Mass: 340.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: tripeptide substrate
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 4.49 Å3/Da / Density % sol: 72.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 42% sat'd ammonium sulfate 0.1M sodium acetate, 10% v/v ethylene glycol, 10 mM Angiotensin II, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2000 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 27730 / Num. obs: 27676 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR
Starting model: 1S2B

1s2b


Resolution: 2→27 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 26254 -Random
Rwork0.234 ---
all-27730 --
obs-27676 94.7 %-
Refinement stepCycle: LAST / Resolution: 2→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 13 121 1606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006

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