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- PDB-8bty: Structure of the active form of ScpB, the C5a-peptidase from Stre... -

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Basic information

Entry
Database: PDB / ID: 8bty
TitleStructure of the active form of ScpB, the C5a-peptidase from Streptococcus agalactiae.
ComponentsC5a peptidase
KeywordsHYDROLASE / C5a-peptidase / virulence factor
Function / homology
Function and homology information


C5a peptidase / serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
CHU_C Type IX secretion signal domain / Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / PA domain superfamily / PA domain / PA domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. ...CHU_C Type IX secretion signal domain / Fn3-like domain / C5a peptidase-like domain / Fn3-like domain / PA domain superfamily / PA domain / PA 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 / 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
MALONIC ACID / C5a peptidase
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKagawa, T.F. / Cooney, J.C. / Miclot, T. / Cullen, R.
Funding support Ireland, 3items
OrganizationGrant numberCountry
Irish Research CouncilRS/2012/391 Ireland
Science Foundation IrelandGrant 12/RC/2275_P2 Ireland
Enterprise IrelandCF/2013/3336 Ireland
Citation
Journal: Proteins / Year: 2024
Title: The 1.7 angstrom crystal structure of the C5a peptidase from Streptococcus agalactiae (ScpB) reveals an active site competent for catalysis.
Authors: Cullen, R. / Tecza, M. / Miclot, T. / Behan, S. / Jain, M. / Avink, M.K. / Cooney, J.C. / Kagawa, T.F.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)221,18817
Polymers219,7262
Non-polymers1,46215
Water11,422634
1
A: C5a peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,32516
Polymers109,8631
Non-polymers1,46215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C5a peptidase


  • defined by author
  • 110 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)109,8631
Polymers109,8631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.152, 167.152, 141.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein C5a peptidase


Mass: 109862.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sample sequence begins with residue N31. Chain B is likely a peptide produced by auto-proteolytic activation of the enzyme. Residues in this chain are in the pro-peptide region. Assignments ...Details: Sample sequence begins with residue N31. Chain B is likely a peptide produced by auto-proteolytic activation of the enzyme. Residues in this chain are in the pro-peptide region. Assignments of density for A84, P85, Q86, and A87 in Chain B are tentative.
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: scpB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q53637

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Non-polymers , 6 types, 649 molecules

#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 2.5 M ammonium sulfate, 0.1 M Hepes/KOH pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→48.253 Å / Num. obs: 127120 / % possible obs: 99.88 % / Redundancy: 40 % / Biso Wilson estimate: 33.63 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.0334 / Rrim(I) all: 0.2124 / Net I/σ(I): 16.63
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 39.6 % / Mean I/σ(I) obs: 0.34 / Num. unique obs: 12428 / CC1/2: 0.237 / CC star: 0.619 / Rpim(I) all: 0.8948 / Rrim(I) all: 5.659 / % possible all: 99.01

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJanuary 31, 2020data reduction
PHASER2.7.17phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EIF

3eif


Resolution: 1.7→44.84 Å / SU ML: 0.3451 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.0543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 12179 5.01 %
Rwork0.1881 230810 -
obs0.1895 126986 99.86 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.65 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7084 0 79 634 7797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00597394
X-RAY DIFFRACTIONf_angle_d0.773310069
X-RAY DIFFRACTIONf_chiral_restr0.05141120
X-RAY DIFFRACTIONf_plane_restr0.0061319
X-RAY DIFFRACTIONf_dihedral_angle_d14.7612676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.5354730.60019022X-RAY DIFFRACTION97.38
1.72-1.750.53984880.48339234X-RAY DIFFRACTION99.92
1.75-1.770.4344860.41749220X-RAY DIFFRACTION99.91
1.77-1.80.37554920.36879197X-RAY DIFFRACTION99.98
1.8-1.830.33774860.32279242X-RAY DIFFRACTION99.94
1.83-1.860.31694870.29789272X-RAY DIFFRACTION99.94
1.86-1.90.33674870.28999233X-RAY DIFFRACTION99.95
1.9-1.930.31224960.30019236X-RAY DIFFRACTION99.96
1.93-1.970.29424830.27439253X-RAY DIFFRACTION99.99
1.97-2.020.29064810.27259255X-RAY DIFFRACTION100
2.02-2.060.25614870.23769237X-RAY DIFFRACTION99.96
2.06-2.110.22994860.21069220X-RAY DIFFRACTION99.93
2.11-2.170.24284850.19269278X-RAY DIFFRACTION100
2.17-2.240.2264890.18579247X-RAY DIFFRACTION99.97
2.24-2.310.24684800.18049195X-RAY DIFFRACTION99.9
2.31-2.390.21574830.17519282X-RAY DIFFRACTION100
2.39-2.490.21784890.18049230X-RAY DIFFRACTION99.99
2.49-2.60.22774920.18469223X-RAY DIFFRACTION100
2.6-2.740.24194930.19269276X-RAY DIFFRACTION100
2.74-2.910.22464800.19939223X-RAY DIFFRACTION100
2.91-3.130.22724900.2019250X-RAY DIFFRACTION99.99
3.13-3.450.20544930.17059226X-RAY DIFFRACTION100
3.45-3.940.16614860.14729257X-RAY DIFFRACTION99.99
3.94-4.970.14294930.12519242X-RAY DIFFRACTION100
4.97-44.840.19234940.16919260X-RAY DIFFRACTION99.91
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)
10.91340255742-0.007520003136330.1534597879090.82805572786-0.01702385305640.7012930128260.0210019158376-0.0801904509678-0.1450534303190.0543731215291-0.03781863052620.007108718040010.0870563758430.04869612331820.01313043104530.246506979918-0.03635433557240.006042511077630.2540875674350.005149938086510.2614404399962.91817298518.229507165783.6257508951
20.496091657928-0.141652749429-0.1630227070261.401656505480.8281130954121.71370214892-0.00384735090260.301323704991-0.140226584791-0.2943890909620.100038925027-0.208079279065-0.02768884661690.2530677592510.04134374903860.343008710234-0.05744233967160.06084098579510.434252227501-0.04193978674160.32773851172480.859728222620.374529316456.4495583934
30.9914657684080.2645232468860.7001993027721.251740749660.5669983947832.0635183058-0.0793946492261-0.01300516768470.129081900223-0.0775638734443-0.01369493637880.17304462293-0.308323929208-0.07500509178570.09611366893940.305553369603-0.00407688819549-0.02121442503350.236779506256-0.01516957008450.3140954566752.484477282943.603058403977.9751406625
41.186655815430.9013040099640.7482178030861.302874334270.8495146719091.58050095482-0.01479976813065.8990755276E-5-0.0262294166707-0.02943648213850.0243652671845-0.01367967739430.104403839855-0.0821289233108-0.015649048050.239365895418-0.007522657325-0.02793102710660.2579877587960.004045825533870.28108855045934.687642072910.70086006151.6736562325
51.39592639911-0.0555986705878-0.01003924965472.550406231621.373709553953.93929886423-0.1010323961880.13504001225-0.128699924042-0.2543031563490.0775391775644-0.1894412667990.2720458977540.09048062836050.01765677898640.369566806243-0.05857817691120.01525991162710.271911599426-0.03205980850560.32984790431632.219243135-5.1091348695726.0239354239
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 97 through 332 or resid 470 through 583 )97 - 5831 - 485
22chain 'A' and (resid 333 through 345 or resid 349 through 469 )333 - 469237 - 371
33chain 'A' and (resid 584 through 712 )584 - 712486 - 614
44chain 'A' and (resid 713 through 802 or resid 806 through 930 )713 - 930615 - 832
55chain 'A' and (resid 931 through 1032)931 - 1032833 - 934

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