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- PDB-5xxz: Crystal structure of a serine protease from Streptococcus species -

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Basic information

Entry
Database: PDB / ID: 5xxz
TitleCrystal structure of a serine protease from Streptococcus species
ComponentsChemokine protease C
KeywordsLYASE / Subtilisin like / Cell adhesion / Protease
Function / homology
Function and homology information


C5a peptidase / serine-type endopeptidase activity / proteolysis / membrane / metal ion binding
Similarity search - Function
Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / PA domain superfamily / PA domain / PA domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. ...Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / PA domain superfamily / PA domain / PA domain / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.085 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Biochem. J. / Year: 2018
Title: Structure of ScpC, a virulence protease fromStreptococcus pyogenes, reveals the functional domains and maturation mechanism.
Authors: Jobichen, C. / Tan, Y.C. / Prabhakar, M.T. / Nayak, D. / Biswas, D. / Pannu, N.S. / Hanski, E. / Sivaraman, J.
History
DepositionJul 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)341,04811
Polymers340,5752
Non-polymers4739
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-55 kcal/mol
Surface area119380 Å2
Unit cell
Length a, b, c (Å)182.134, 132.847, 151.989
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chemokine protease C


Mass: 170287.469 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 115-1647 / Mutation: H279A, S617A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: scpC / Production host: Escherichia coli (E. coli) / References: UniProt: Q3HV58
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca

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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: 2.49 Å3/Da / Density % sol: 50.62 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.65
Details: 0.2 M MgCl hexahydrate, 0.1 M Tris, pH 8.65, 28% PEG 3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 126754 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 10
Reflection shellResolution: 3.08→3.12 Å / Rmerge(I) obs: 0.72

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.085→19.979 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.93
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.263 3891 3.07 %
Rwork0.2055 --
obs0.2073 126754 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.085→19.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19898 0 17 0 19915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01220278
X-RAY DIFFRACTIONf_angle_d1.36227463
X-RAY DIFFRACTIONf_dihedral_angle_d3.64612100
X-RAY DIFFRACTIONf_chiral_restr0.0683074
X-RAY DIFFRACTIONf_plane_restr0.0093596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0853-3.12280.31061170.29643823X-RAY DIFFRACTION86
3.1228-3.16210.37851340.29284237X-RAY DIFFRACTION95
3.1621-3.20360.34521380.28974332X-RAY DIFFRACTION97
3.2036-3.24730.37551400.28464347X-RAY DIFFRACTION98
3.2473-3.29350.31831400.27044343X-RAY DIFFRACTION99
3.2935-3.34240.32041410.26574380X-RAY DIFFRACTION99
3.3424-3.39440.31791420.25094389X-RAY DIFFRACTION99
3.3944-3.44980.29741390.24434421X-RAY DIFFRACTION99
3.4498-3.5090.31881410.24424451X-RAY DIFFRACTION99
3.509-3.57240.25871360.2244398X-RAY DIFFRACTION99
3.5724-3.64070.25441430.21834471X-RAY DIFFRACTION100
3.6407-3.71460.22431400.20894385X-RAY DIFFRACTION100
3.7146-3.79480.27161380.21074446X-RAY DIFFRACTION100
3.7948-3.88250.27081450.20954461X-RAY DIFFRACTION100
3.8825-3.97880.3011380.20434385X-RAY DIFFRACTION100
3.9788-4.08550.27671380.19384403X-RAY DIFFRACTION100
4.0855-4.20460.26831410.19434501X-RAY DIFFRACTION100
4.2046-4.3390.26561380.17394406X-RAY DIFFRACTION100
4.339-4.49240.21081400.16644435X-RAY DIFFRACTION100
4.4924-4.67010.19451410.15844458X-RAY DIFFRACTION100
4.6701-4.87970.20861420.1584410X-RAY DIFFRACTION100
4.8797-5.13280.22151400.16814440X-RAY DIFFRACTION100
5.1328-5.44830.19851400.17624425X-RAY DIFFRACTION100
5.4483-5.85910.24431390.18264427X-RAY DIFFRACTION100
5.8591-6.43080.22681410.19624406X-RAY DIFFRACTION100
6.4308-7.3210.24531400.20084440X-RAY DIFFRACTION100
7.321-9.07730.28741390.19444392X-RAY DIFFRACTION99
9.0773-19.9790.27731400.21554451X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.011 Å / Origin y: 100.8158 Å / Origin z: 107.9248 Å
111213212223313233
T0.324 Å20.0122 Å2-0.0693 Å2-0.4949 Å2-0.059 Å2--0.3196 Å2
L0.1533 °20.0192 °20.0561 °2-0.2798 °20.0304 °2--0.1025 °2
S0.0037 Å °-0.0456 Å °0.0416 Å °0.0053 Å °-0.0147 Å °0.018 Å °-0.018 Å °-0.029 Å °0.012 Å °
Refinement TLS groupSelection details: ALL

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