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- PDB-8oig: Crystal Structure of Staphopain C from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 8oig
TitleCrystal Structure of Staphopain C from Staphylococcus aureus
ComponentsThiol protease
KeywordsHYDROLASE / cystein protease / thiol protease / papain-fold / staphopain
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis / extracellular region
Similarity search - Function
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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMcEwen, A.G. / Magoch, M. / Napolitano, V. / Dubin, G. / Wladyka, B.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2011/01/D/NZ1/01169 Poland
Polish National Science CentreN N303 813340 Poland
CitationJournal: Molecules / Year: 2023
Title: Crystal Structure of Staphopain C from Staphylococcus aureus.
Authors: Magoch, M. / McEwen, A.G. / Napolitano, V. / Wladyka, B. / Dubin, G.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol protease
B: Thiol protease
C: Thiol protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,46113
Polymers58,9103
Non-polymers55110
Water7,945441
1
A: Thiol protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8213
Polymers19,6371
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7083
Polymers19,6371
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thiol protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9337
Polymers19,6371
Non-polymers2966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.136, 103.136, 51.204
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Thiol protease


Mass: 19636.686 Da / Num. of mol.: 3 / Mutation: D101G / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q8RJP3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M AmSO4, 0.1M Tris, ph 8.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.05 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.58→51.57 Å / Num. obs: 80816 / % possible obs: 97.59 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.07
Reflection shellResolution: 1.582→1.639 Å / Num. unique obs: 8329 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→51.57 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.322 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.008 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.11597 2024 2.5 %RANDOM
Rwork0.08754 ---
obs0.08824 78756 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.511 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20 Å2
2---1.08 Å20 Å2
3---2.15 Å2
Refinement stepCycle: 1 / Resolution: 1.58→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 28 441 4585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0114288
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163966
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.6535814
X-RAY DIFFRACTIONr_angle_other_deg0.6411.5928945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.374525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64410698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021112
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.050.8492089
X-RAY DIFFRACTIONr_mcbond_other1.0470.8492089
X-RAY DIFFRACTIONr_mcangle_it1.5641.5272610
X-RAY DIFFRACTIONr_mcangle_other1.5641.5272611
X-RAY DIFFRACTIONr_scbond_it1.6291.0082199
X-RAY DIFFRACTIONr_scbond_other1.6291.0082200
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4131.7713197
X-RAY DIFFRACTIONr_long_range_B_refined4.0489.845033
X-RAY DIFFRACTIONr_long_range_B_other3.9088.984926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.582→1.623 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.111 108 -
Rwork0.089 5966 -
obs--98.25 %
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)
12.02290.02530.37530.6241-0.26230.6941-0.0203-0.0343-0.1239-0.00020.0567-0.01020.0472-0.0075-0.03640.02460.0078-0.00160.0158-0.00240.0093-48.45973.85516.42
20.95490.0437-0.42971.48030.13280.8860.04280.04610.0369-0.00890.0001-0.12510.01780.0319-0.04290.00860.00040.00090.04160.00110.0128-36.50433.97928.312
31.3751-0.55930.03221.5041-0.45590.77150.03790.0282-0.07920.05660.00880.06890.0341-0.0256-0.04670.0191-0.003-0.00290.0026-0.00010.0073-11.29148.6577.614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A301 - 399
2X-RAY DIFFRACTION2B301 - 399
3X-RAY DIFFRACTION3C301 - 399

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