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

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Basic information

Entry
Database: PDB / ID: 5xya
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 ...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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Gram-positive cocci surface proteins LPxTG motif profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / LPXTG cell wall anchor domain / Subtilase family / Immunoglobulin-like fold
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / C5a peptidase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 6, 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
Revision 1.2Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemokine protease C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7359
Polymers170,0831
Non-polymers6528
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-72 kcal/mol
Surface area60350 Å2
Unit cell
Length a, b, c (Å)190.530, 190.530, 248.668
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Chemokine protease C


Mass: 170083.203 Da / Num. of mol.: 1
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-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 40.078 Da / Num. of mol.: 4 / 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: 3.59 Å3/Da / Density % sol: 65.76 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MgCl hexahydrate, 0.1 M Tris, pH 8.65, and 28% PEG3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 104019 / % possible obs: 98.9 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 18
Reflection shellResolution: 2.9→2.976 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 3471

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_2733phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XXZ

5xxz


Resolution: 3→19.899 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 3592 3.59 %
Rwork0.2225 --
obs0.2245 100165 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→19.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10273 0 31 0 10304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310502
X-RAY DIFFRACTIONf_angle_d1.42314237
X-RAY DIFFRACTIONf_dihedral_angle_d4.3296272
X-RAY DIFFRACTIONf_chiral_restr0.0691592
X-RAY DIFFRACTIONf_plane_restr0.0081863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03940.38071260.33123345X-RAY DIFFRACTION89
3.0394-3.08080.33691330.32653622X-RAY DIFFRACTION97
3.0808-3.12470.38841390.3233700X-RAY DIFFRACTION99
3.1247-3.17120.34461400.30293734X-RAY DIFFRACTION100
3.1712-3.22050.34151360.29773724X-RAY DIFFRACTION100
3.2205-3.27310.29831390.283769X-RAY DIFFRACTION100
3.2731-3.32930.33321370.26953724X-RAY DIFFRACTION100
3.3293-3.38950.29441380.25733727X-RAY DIFFRACTION100
3.3895-3.45440.32181430.25293736X-RAY DIFFRACTION100
3.4544-3.52450.34091370.24073748X-RAY DIFFRACTION100
3.5245-3.60070.2541370.23313749X-RAY DIFFRACTION100
3.6007-3.6840.28711410.22433715X-RAY DIFFRACTION100
3.684-3.77550.29711430.22353726X-RAY DIFFRACTION100
3.7755-3.87680.27861380.22693761X-RAY DIFFRACTION100
3.8768-3.990.31431400.21563706X-RAY DIFFRACTION100
3.99-4.11770.26191460.21173733X-RAY DIFFRACTION100
4.1177-4.26350.25571370.2033736X-RAY DIFFRACTION100
4.2635-4.43240.24171360.18583755X-RAY DIFFRACTION100
4.4324-4.63170.25261420.18513732X-RAY DIFFRACTION100
4.6317-4.87250.21511360.1763737X-RAY DIFFRACTION100
4.8725-5.17280.25191360.17673728X-RAY DIFFRACTION100
5.1728-5.56410.24281350.17653743X-RAY DIFFRACTION100
5.5641-6.10920.22961420.17863739X-RAY DIFFRACTION100
6.1092-6.95990.25821400.19293734X-RAY DIFFRACTION100
6.9599-8.64730.24051420.19173758X-RAY DIFFRACTION100
8.6473-19.8990.22471330.18343692X-RAY DIFFRACTION99

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