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- PDB-1x9y: The prostaphopain B structure -

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Basic information

Entry
Database: PDB / ID: 1x9y
TitleThe prostaphopain B structure
Componentscysteine proteinase
KeywordsHYDROLASE / half-barrel / barrel-sandwich-hybrid
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region
Similarity search - Function
prostaphopain b, domain 1 / Staphopain proregion domain / Staphopain peptidase C47 / Staphopain proregion / Staphopain proregion superfamily / Staphopain peptidase C47 / Staphopain proregion / Cystatin superfamily / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...prostaphopain b, domain 1 / Staphopain proregion domain / Staphopain peptidase C47 / Staphopain proregion / Staphopain proregion superfamily / Staphopain peptidase C47 / Staphopain proregion / Cystatin superfamily / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Staphopain B / Staphopain B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFilipek, R. / Szczepanowski, R. / Sabat, A. / Potempa, J. / Bochtler, M.
Citation
Journal: Biochemistry / Year: 2004
Title: Prostaphopain B structure: a comparison of proregion-mediated and staphostatin-mediated protease inhibition.
Authors: Filipek, R. / Szczepanowski, R. / Sabat, A. / Potempa, J. / Bochtler, M.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease.
Authors: Filipek, R. / Rzychon, M. / Oleksy, A. / Gruca, M. / Dubin, A. / Potempa, J. / Bochtler, M.
History
DepositionAug 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cysteine proteinase
B: cysteine proteinase
C: cysteine proteinase
D: cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)167,3864
Polymers167,3864
Non-polymers00
Water4,378243
1
A: cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)41,8471
Polymers41,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)41,8471
Polymers41,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)41,8471
Polymers41,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cysteine proteinase


Theoretical massNumber of molelcules
Total (without water)41,8471
Polymers41,8471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.621, 104.918, 173.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe protein is a monomer

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Components

#1: Protein
cysteine proteinase


Mass: 41846.504 Da / Num. of mol.: 4 / Fragment: proenzyme (residues 37-393)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sspB / Plasmid: pGEX-5T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q70UQ8, UniProt: P0C1S6*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.47 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 4000, 50 mM Bis-Tris, 5 mM Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 9, 2003 / Details: MSC Confocal MaxFlux mirrors
RadiationMonochromator: MSC Confocal MaxFlux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 53566 / Num. obs: 53566 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3 / Num. unique all: 2535 / Rsym value: 0.339 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PXV

1pxv


Resolution: 2.5→19.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2479432.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2730 5.1 %RANDOM
Rwork0.244 ---
all0.246 53496 --
obs0.244 53496 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.0088 Å2 / ksol: 0.311264 e/Å3
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1--10.55 Å20 Å20 Å2
2---9.81 Å20 Å2
3---20.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11112 0 0 243 11355
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.662.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 438 5 %
Rwork0.342 8237 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.PARAM

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