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- PDB-5jd8: Crystal structure of the serine endoprotease from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 5jd8
TitleCrystal structure of the serine endoprotease from Yersinia pestis
ComponentsPeriplasmic serine peptidase DegS
KeywordsHYDROLASE / DegS / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein quality control for misfolded or incompletely synthesized proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / periplasmic space / serine-type endopeptidase activity
Similarity search - Function
Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / Protease
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFilippova, E.V. / Wawrzsak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of the serine endoprotease from Yersinia pestis
Authors: Filippova, E.V. / Wawrzsak, Z. / Sandoval, J. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine peptidase DegS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7784
Polymers35,3551
Non-polymers4243
Water2,774154
1
A: Periplasmic serine peptidase DegS
hetero molecules

A: Periplasmic serine peptidase DegS
hetero molecules

A: Periplasmic serine peptidase DegS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,33512
Polymers106,0643
Non-polymers1,2719
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8430 Å2
ΔGint-77 kcal/mol
Surface area37040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.418, 104.418, 76.015
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-403-

SO4

21A-553-

HOH

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Components

#1: Protein Periplasmic serine peptidase DegS


Mass: 35354.785 Da / Num. of mol.: 1 / Fragment: UNP residues 29-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: degS, AK38_3169 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A0B6NK33, UniProt: A0A5P8YL96*PLUS
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 10% Isopropane, 50 mM CAPSO buffer pH 11, 0.1 M Sodium citrate pH 5.6, 5% P200 paratone-N oil

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2016 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 26479 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RQY

4rqy


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.311 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18269 1292 4.9 %RANDOM
Rwork0.14831 ---
obs0.14999 25187 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 26 154 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192081
X-RAY DIFFRACTIONr_bond_other_d0.0020.022115
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9852828
X-RAY DIFFRACTIONr_angle_other_deg1.04834843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2365271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47525.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8461513
X-RAY DIFFRACTIONr_chiral_restr0.1280.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212347
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02424
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_it2.3333.2341093
X-RAY DIFFRACTIONr_mcbond_other2.3313.2331092
X-RAY DIFFRACTIONr_mcangle_it3.8094.8151361
X-RAY DIFFRACTIONr_mcangle_other3.8084.8171362
X-RAY DIFFRACTIONr_scbond_it2.8893.643988
X-RAY DIFFRACTIONr_scbond_other2.8813.627984
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6135.2931462
X-RAY DIFFRACTIONr_long_range_B_refined7.96825.6242188
X-RAY DIFFRACTIONr_long_range_B_other7.96625.6312189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 91 -
Rwork0.201 1871 -
obs--99.09 %
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)
10.6618-0.9985-0.42221.65350.56670.62750.02690.01320.0847-0.0401-0.0615-0.22940.0304-0.00330.03460.04490.01770.03520.05820.01170.129520.700747.065650.4939
20.9328-0.3613-0.08210.39450.03660.08660.01290.0397-0.1135-0.0398-0.019-0.0138-0.0046-0.00390.00610.06950.00860.01090.05810.00660.09017.210849.353553.9369
31.71290.6593-1.14710.73040.17061.5592-0.2290.1031-0.29190.0298-0.0235-0.07310.3011-0.17170.25260.1153-0.00680.07280.0315-0.0080.20810.953229.217249.0316
41.8574-1.07562.36756.53031.62164.65320.2295-0.0797-0.3372-0.2508-0.12170.62360.35-0.3537-0.10780.1449-0.16960.05250.2412-0.14440.1847-3.274315.748739.0372
510.2623-5.71640.22315.61931.6171.35820.0425-0.2805-0.11010.1902-0.12190.05460.27-0.30070.07940.1491-0.12940.08630.1241-0.07140.07592.278521.22447.5389
612.27440.10955.24830.29730.0630.0736-0.0238-0.34470.1557-0.114-0.69020.0572-0.11960.04040.1592-0.20960.00990.3536-0.13330.2497-6.77138.28442.0678
74.47553.12640.37146.89921.06350.34420.08620.7828-0.39540.47810.0299-0.04220.17370.1044-0.11610.18690.0306-0.00060.2864-0.18810.16148.261916.176642.7082
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 134
2X-RAY DIFFRACTION2A135 - 234
3X-RAY DIFFRACTION3A235 - 263
4X-RAY DIFFRACTION4A280 - 311
5X-RAY DIFFRACTION5A312 - 329
6X-RAY DIFFRACTION6A330 - 343
7X-RAY DIFFRACTION7A344 - 351

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