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- PDB-1pvj: Crystal structure of the Streptococcal pyrogenic exotoxin B (SpeB... -

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Basic information

Entry
Database: PDB / ID: 1pvj
TitleCrystal structure of the Streptococcal pyrogenic exotoxin B (SpeB)- inhibitor complex
Componentspyrogenic exotoxin B
KeywordsTOXIN / Streptococcus pyogenes exotoxin(SpeB) / Z-F-CH2N2- benzyloxycarbonyl phenylalanyl alanyl diazomethane.
Function / homology
Function and homology information


streptopain / symbiont-mediated suppression of host autophagy / symbiont-induced defense-related programmed cell death / evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Peptidase C10 family / Protein Binding, DinI Protein; Chain A / Peptidase C10, streptopain superfmaily / Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10 family / Streptopain (SpeB) / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily ...Peptidase C10 family / Protein Binding, DinI Protein; Chain A / Peptidase C10, streptopain superfmaily / Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10 family / Streptopain (SpeB) / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZFB / Streptopain
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZiomek, E. / Sivaraman, J. / Doran, J. / Menard, R. / Cygler, M.
CitationJournal: To be published
Title: Inhibition of autoprocessing of the streptococcal pyrogenic exotoxin B (speB). Crystal structure of the proenzyme-inhibitor complex
Authors: Ziomek, E. / Sivaraman, J. / Doran, J. / Menard, R. / Cygler, M.
History
DepositionJun 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Remark 600MISSING LIGAND ATOMS Atoms N2, N3 for ligand ZFB missing due to reaction with SG of CYS47, ...MISSING LIGAND ATOMS Atoms N2, N3 for ligand ZFB missing due to reaction with SG of CYS47, resulting in covalent bond formation between SG of CYS47 and C11 of ZFB
Remark 999PROREGION Residues 31-139 represent the proregion of this protease

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pyrogenic exotoxin B
B: pyrogenic exotoxin B
C: pyrogenic exotoxin B
D: pyrogenic exotoxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3838
Polymers160,0854
Non-polymers1,2974
Water9,944552
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.769, 119.495, 144.083
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
pyrogenic exotoxin B


Mass: 40021.281 Da / Num. of mol.: 4 / Fragment: Streptococcal Pyrogenic Exotoxin B (SpeB) / Source method: isolated from a natural source / Source: (natural) Streptococcus pyogenes (bacteria) / Strain: B220PTPRC / References: UniProt: P0C0J0, streptopain
#2: Chemical
ChemComp-ZFB / (3R)-3-{[(BENZYLOXY)CARBONYL]AMINO}-2-OXO-4-PHENYLBUTANE-1-DIAZONIUM


Type: L-peptide linking / Mass: 324.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18N3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Ammonium Sulphate, Glycerol, Sodium citrate, PEG 8K, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2001
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 29796 / Num. obs: 29796 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.139
Reflection shellResolution: 3→3.11 Å / Rsym value: 0.367 / % possible all: 95.4

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Processing

Software
NameClassification
Adxvdata processing
HKL-2000data reduction
AMoREphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 1613 RANDAM
Rwork0.227 --
all-29796 -
obs-23696 -
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10412 0 88 552 11052
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_d1.7

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