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- PDB-1pxv: The staphostatin-staphopain complex: a forward binding inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 1pxv
TitleThe staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease
Components
  • cysteine protease
  • cysteine protease Inhibitor
KeywordsHYDROLASE / cysteine protease inhibitor
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / cytoplasm
Similarity search - Function
Staphostatin B / Staphostatin B / Staphostatins / beta-Barrel protease inhibitors / Staphopain peptidase C47 / Staphopain proregion / Staphopain proregion superfamily / Staphostatin A/B / Staphopain peptidase C47 / Staphopain proregion ...Staphostatin B / Staphostatin B / Staphostatins / beta-Barrel protease inhibitors / Staphopain peptidase C47 / Staphopain proregion / Staphopain proregion superfamily / Staphostatin A/B / Staphopain peptidase C47 / Staphopain proregion / Protease inhibitor, beta-barrel domain / 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 / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANIDINE / Staphopain B / Staphopain B / Staphostatin B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFilipek, R. / Rzychon, M. / Oleksy, A. / Gruca, M. / Dubin, A. / Potempa, J. / Bochtler, M.
Citation
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.
#1: Journal: Protein Sci. / Year: 2003
Title: Staphostatins resemble lipocalins, not cystatins in fold.
Authors: Rzychon, M. / Filipek, R. / Sabat, A. / Kosowska, K. / Dubin, A. / Potempa, J. / Bochtler, M.
#2: Journal: MOL.MICROBIOL. / Year: 2003
Title: Staphostatins: an expanding new group of proteinase inhibitors with a unique specificity for the regulation of staphopains, Staphylococcus spp. cysteine proteinases
Authors: Rzychon, M. / Sabat, A. / Kosowska, K. / Potempa, J. / Dubin, A.
#3: Journal: J.Biol.Chem. / Year: 2002
Title: Identification of a novel maturation mechanism and restricted substrate specificity for the SspB cysteine protease of Staphylococcus aureus
Authors: Massimi, I. / Park, E. / Rice, K. / Muller-Esterl, W. / Sauder, D. / McGavin, M.J.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE At the time of processing, there was no database sequence available for the proteins from ...SEQUENCE At the time of processing, there was no database sequence available for the proteins from Staphylococcus aureus, strain V8 that were crystallized here. The closest homologues with protein sequences in a database were from Staphylococcus aureus subsp. aureus MW2. The author claims that the residue conflicts between strain V8 and strain MW2 noted here are genuine, confirmed strain differences.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cysteine protease
B: cysteine protease
C: cysteine protease Inhibitor
D: cysteine protease Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81310
Polymers68,2734
Non-polymers5396
Water8,251458
1
A: cysteine protease
C: cysteine protease Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4255
Polymers34,1372
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-37 kcal/mol
Surface area15040 Å2
MethodPISA
2
B: cysteine protease
D: cysteine protease Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3885
Polymers34,1372
Non-polymers2513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-50 kcal/mol
Surface area15200 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-111 kcal/mol
Surface area27300 Å2
MethodPISA
4
B: cysteine protease
D: cysteine protease Inhibitor
hetero molecules

A: cysteine protease
C: cysteine protease Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81310
Polymers68,2734
Non-polymers5396
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7290 Å2
ΔGint-97 kcal/mol
Surface area28750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.485, 94.966, 110.927
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 cysteine protease


Mass: 21062.078 Da / Num. of mol.: 2 / Mutation: C243A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: staphopain B / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3)
References: UniProt: Q70UQ8, UniProt: P0C1S6*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein cysteine protease Inhibitor


Mass: 13074.622 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: staphostatin B / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3)[pLysS]
References: UniProt: Q9EYW6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 2 M (NH4)2SO4 and 5% isopropanol, 100 mM guanidinium hydrochloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
25 %isopropyl alcohol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.8→20.92 Å / Num. all: 72496 / Num. obs: 66436 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3959 / Rsym value: 0.182 / % possible all: 89.3
Reflection
*PLUS
Num. obs: 64796 / % possible obs: 92 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
FFFEARphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CV8, 1NYC

1cv8

1nyc


Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22129 3406 5 %RANDOM
Rwork0.19055 ---
all0.1921 64796 --
obs0.1921 64796 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 29 458 5303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214867
X-RAY DIFFRACTIONr_bond_other_d00.024032
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9126610
X-RAY DIFFRACTIONr_angle_other_deg3.93539405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6445583
X-RAY DIFFRACTIONr_chiral_restr0.1170.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025515
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02975
X-RAY DIFFRACTIONr_nbd_refined0.240.2955
X-RAY DIFFRACTIONr_nbd_other0.310.24600
X-RAY DIFFRACTIONr_nbtor_other0.1150.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2383
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3710.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.213
X-RAY DIFFRACTIONr_mcbond_it1.9331.52921
X-RAY DIFFRACTIONr_mcangle_it3.03224690
X-RAY DIFFRACTIONr_scbond_it2.27231946
X-RAY DIFFRACTIONr_scangle_it3.4734.51920
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 214
Rwork0.227 4300
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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