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- PDB-2ifw: Crystal structure of scytalido-glutamic peptidase with a transiti... -

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Basic information

Entry
Database: PDB / ID: 2ifw
TitleCrystal structure of scytalido-glutamic peptidase with a transition state analog inhibitor
Components
  • Heptapeptide
  • Scytalidopepsin B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / enzyme-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR complex
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
ACETIC ACID / Scytalidopepsin B
Similarity search - Component
Biological speciesScytalidium lignicola (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPillai, B. / Cherney, M.M. / Hiraga, K. / Takada, K. / Oda, K. / James, M.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of scytalidoglutamic peptidase with its first potent inhibitor provides insights into substrate specificity and catalysis.
Authors: Pillai, B. / Cherney, M.M. / Hiraga, K. / Takada, K. / Oda, K. / James, M.N.
History
DepositionSep 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 30, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Scytalidopepsin B
C: Heptapeptide
D: Heptapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2688
Polymers44,9644
Non-polymers3044
Water2,000111
1
A: Scytalidopepsin B
C: Heptapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6344
Polymers22,4822
Non-polymers1522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-9 kcal/mol
Surface area8570 Å2
MethodPISA
2
B: Scytalidopepsin B
D: Heptapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6344
Polymers22,4822
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-8 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.563, 55.211, 151.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21553.812 Da / Num. of mol.: 2
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 Heptapeptide


Mass: 928.174 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3300, 0.2 M NaCl, 0.1 M Bis-Tris buffer, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 20, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 17716 / Num. obs: 17716 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 96.5

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Processing

Software
NameClassification
Blu-Icedata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1S2B

1s2b


Resolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 890 -random
Rwork0.221 ---
all0.265 17716 --
obs0.265 17716 98.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 20 111 3289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.72

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