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- PDB-1y4h: Wild type staphopain-staphostatin complex -

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Basic information

Entry
Database: PDB / ID: 1y4h
TitleWild type staphopain-staphostatin complex
Components
  • cysteine protease
  • cysteine protease inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine protease / inhibitor / staphopain B / staphostatin B / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
Staphopain B / Staphopain B / Staphostatin B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsFilipek, R. / Potempa, J. / Bochtler, M.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: A comparison of staphostatin B with standard mechanism serine protease inhibitors.
Authors: Filipek, R. / 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.
#2: 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.
#3: 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.
#4: 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.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 23, 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_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

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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)69,58413
Polymers68,9624
Non-polymers6229
Water3,063170
1
A: cysteine protease
C: cysteine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9729
Polymers34,4812
Non-polymers4917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-64 kcal/mol
Surface area13700 Å2
MethodPISA
2
B: cysteine protease
D: cysteine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6134
Polymers34,4812
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-27 kcal/mol
Surface area13720 Å2
MethodPISA
3
A: cysteine protease
C: cysteine protease inhibitor
hetero molecules

B: cysteine protease
D: cysteine protease inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,58413
Polymers68,9624
Non-polymers6229
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area6940 Å2
ΔGint-105 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.948, 77.520, 84.891
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cysteine protease / staphopain B


Mass: 21550.619 Da / Num. of mol.: 2 / Fragment: residues 220-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sspB / Plasmid: pETDuet / 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: Protein cysteine protease inhibitor / staphostatin B


Mass: 12930.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sspC / Plasmid: pETDuet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9EYW6
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 2M (NH4)2SO4, 9% isopropanol , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K

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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: Jul 21, 2004 / Details: MONOCHROMATIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. all: 53525 / Num. obs: 53525 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 30
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2087 / Rsym value: 0.32 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PXV

1pxv


Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.608 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21666 2716 5.1 %RANDOM
Rwork0.18829 ---
all0.18972 50784 --
obs0.18972 50784 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.903 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å2-0.05 Å2
2--0.2 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4614 0 29 170 4813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214742
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9266446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65125.53264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8815792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7541516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023688
X-RAY DIFFRACTIONr_nbd_refined0.2040.21851
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23172
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.27
X-RAY DIFFRACTIONr_mcbond_it1.6051.52906
X-RAY DIFFRACTIONr_mcangle_it1.83824558
X-RAY DIFFRACTIONr_scbond_it3.13632133
X-RAY DIFFRACTIONr_scangle_it4.5684.51888
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 193 -
Rwork0.238 3740 -
obs--99.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82150.02610.19171.67310.02182.3747-0.07780.17970.0081-0.35560.07970.1153-0.0833-0.1799-0.0019-0.0059-0.0301-0.01470.07490.0198-0.151313.9786.1559.394
20.88610.09860.17911.4996-0.73984.2049-0.02450.04030.095-0.150.1553-0.0202-0.5001-0.4095-0.1307-0.02110.08470.0373-0.01580.0296-0.093329.8134.9223.064
31.20270.6737-1.07061.9436-0.82832.25260.0077-0.109-0.127-0.1042-0.1144-0.05470.10570.3230.1067-0.08590.01940.02020.06260.0145-0.111117.752-10.86530.4
44.34160.4826-0.39811.5743-0.28112.60310.1579-0.3104-0.23490.0712-0.0706-0.14890.2070.3711-0.0873-0.09810.0543-0.0270.0414-0.0189-0.056745.09520.25840.912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA221 - 39316 - 188
2X-RAY DIFFRACTION2BB221 - 39316 - 188
3X-RAY DIFFRACTION3CC1 - 1091 - 109
4X-RAY DIFFRACTION4DD1 - 1091 - 109

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