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- PDB-2uzj: Crystal structure of the mature streptococcal cysteine protease, mSpeB -

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Basic information

Entry
Database: PDB / ID: 2uzj
TitleCrystal structure of the mature streptococcal cysteine protease, mSpeB
ComponentsSTREPTOPAIN
KeywordsHYDROLASE / PROTEINASE / PAPAIN FAMILY / CYSTEINE PROTEASE / DIMER / CLAN CA / EXOTOXIN / FAMILY 10 / PEPTIDASE
Function / homology
Function and homology information


: / streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / symbiont-mediated evasion of host immune response / host cell cytosol / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity ...: / streptopain / symbiont-induced defense-related programmed cell death / symbiont-mediated suppression of host autophagy / symbiont-mediated 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
Spi protease inhibitor / Spi protease inhibitor / Peptidase C10, streptopain / Peptidase C10, streptopain superfmaily / Peptidase C10 family / Streptopain (SpeB) / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-E64 / Streptopain / Streptopain
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOlsen, J.G. / Dagil, R. / Niclasen, L.M. / Soerensen, O.E. / Kragelund, B.B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of the Mature Streptococcal Cysteine Protease Exotoxin Mspeb in its Active Dimeric Form.
Authors: Olsen, J.G. / Dagil, R. / Niclasen, L.M. / Soerensen, O.E. / Kragelund, B.B.
History
DepositionSep 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STREPTOPAIN
B: STREPTOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9444
Polymers55,2232
Non-polymers7212
Water5,999333
1
A: STREPTOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9722
Polymers27,6121
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: STREPTOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9722
Polymers27,6121
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.828, 60.888, 70.365
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein STREPTOPAIN / MATURE STREPTOCOCCAL PYROGENIC EXOTOXIN B / STREPTOCOCCAL CYSTEINE PROTEINASE / STREPTOCOCCUS ...MATURE STREPTOCOCCAL PYROGENIC EXOTOXIN B / STREPTOCOCCAL CYSTEINE PROTEINASE / STREPTOCOCCUS PEPTIDASE A / SPP / EXOTOXIN TYPE B / SPE B


Mass: 27611.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PROTEIN WAS PURIFIED FROM NATURAL SOURCE. / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / Strain: ALAB49
References: UniProt: Q5X9P3, UniProt: P0C0J0*PLUS, streptopain
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.08 Å3/Da / Density % sol: 40.52 %
Description: MOLECULAR REPLACEMENT SEARCH MODEL WAS 1DKI WITHOUT THE PROPEPTIDE
Crystal growDetails: 0.2 M (NH4)2SO4, 0.1 M NA-ACETATE, PH 4.0, 20 % PEG4000. PROTEIN KONCENTRATION WAS 0.07 MM (IN 20 MM NA-ACETATE, PH 5.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 2008 / Details: MIRRORS. MSC-CONFOCAL MAXFLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→21.48 Å / Num. obs: 63795 / % possible obs: 90.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.32
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 0.97 / % possible all: 55.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKI

1dki


Resolution: 1.55→21.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.602 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 234A-237A AND 234B-239B ARE ABSENT IN THE MODEL BECAUSE OF INSUFFICIENT ELECTRON DENSITY IN THESE REGIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3238 5.1 %RANDOM
Rwork0.181 ---
obs0.183 60554 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.01 Å2
2---0.05 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 50 333 4238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224007
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9375424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67624.949198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4815608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6331514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023172
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21999
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22774
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3251.52495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85523914
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.13431731
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4094.51510
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.444 122
Rwork0.367 2356

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