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- PDB-1xf1: Structure of C5a peptidase- a key virulence factor from Streptococcus -

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Basic information

Entry
Database: PDB / ID: 1xf1
TitleStructure of C5a peptidase- a key virulence factor from Streptococcus
ComponentsC5a peptidase
KeywordsHYDROLASE / C5a peptidase
Function / homology
Function and homology information


C5a peptidase / toxin activity / symbiont-mediated suppression of host innate immune response / serine-type endopeptidase activity / proteolysis / extracellular region / membrane
Similarity search - Function
Subtilisin-like superfamily / : / CHU_C Type IX secretion signal domain / C5a peptidase, fibronectin type III domain / Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain ...Subtilisin-like superfamily / : / CHU_C Type IX secretion signal domain / C5a peptidase, fibronectin type III domain / Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Glucose Oxidase; domain 1 / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / 3-Layer(bba) Sandwich / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / C5a peptidase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBrown, C.K. / Gu, Z.Y. / Cleary, P.P. / Matsuka, Y. / Olmstead, S. / Ohlendorf, D.H. / Earhart, C.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of the streptococcal cell wall C5a peptidase
Authors: Brown, C.K. / Gu, Z.Y. / Matsuka, Y.V. / Purushothaman, S.S. / Winter, L.A. / Cleary, P.P. / Olmsted, S.B. / Ohlendorf, D.H. / Earhart, C.A.
History
DepositionSep 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN CIT 1101, 1103, 1105, ACT 1107, and CA 1109 are associated with protein chain A. CIT ...HETEROGEN CIT 1101, 1103, 1105, ACT 1107, and CA 1109 are associated with protein chain A. CIT 1102, 1104, 1106, ACT 1108, and CA 1110 are associated with protein chain B.
Remark 999SEQUENCE The author states that the residues at 648, 697, and 794 are indeed THR, THR, and PHE, ...SEQUENCE The author states that the residues at 648, 697, and 794 are indeed THR, THR, and PHE, respectively. There is an error in the database sequence.'

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C5a peptidase
B: C5a peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,34312
Polymers205,9922
Non-polymers1,35110
Water19,0421057
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-27 kcal/mol
Surface area76420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.696, 75.113, 132.391
Angle α, β, γ (deg.)90.00, 104.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C5a peptidase / SCP


Mass: 102996.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: scpA / Production host: Escherichia coli (E. coli)
References: UniProt: P15926, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1057 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.5 / Details: pH 4.5, VAPOR DIFFUSION, , temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 171036 / % possible obs: 99.8 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.269 8618 0.05 %
Rwork0.229 --
all-171293 -
obs-171036 -
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14364 0 88 1057 15509
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.491.5
X-RAY DIFFRACTIONo_mcangle_it2.3982
X-RAY DIFFRACTIONo_scbond_it2.3172
X-RAY DIFFRACTIONo_scangle_it3.3242.5

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