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- PDB-4n31: Structure and activity of Streptococcus pyogenes SipA: a signal p... -

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Basic information

Entry
Database: PDB / ID: 4n31
TitleStructure and activity of Streptococcus pyogenes SipA: a signal peptidase homologue essential for pilus polymerisation
ComponentsSipA
KeywordsCELL ADHESION / Streptococcus pyogenes / pilus polymerisation / Signal peptidase family / Pilin assembly protein / Bacterial cell membrane / extracellular
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / serine-type endopeptidase activity / plasma membrane
Similarity search - Function
Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / PHOSPHATIDYLETHANOLAMINE / Signal peptidase I
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYoung, P.G. / Proft, T. / Baker, E.N.
CitationJournal: Plos One / Year: 2014
Title: Structure and activity of Streptococcus pyogenes SipA: a signal peptidase-like protein essential for pilus polymerisation.
Authors: Young, P.G. / Proft, T. / Harris, P.W. / Brimble, M.A. / Baker, E.N.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SipA
B: SipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1985
Polymers37,2742
Non-polymers9243
Water1,35175
1
A: SipA
B: SipA
hetero molecules

A: SipA
B: SipA
hetero molecules

A: SipA
B: SipA
hetero molecules

A: SipA
B: SipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,79120
Polymers149,0958
Non-polymers3,69612
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area21750 Å2
ΔGint-200 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.811, 132.811, 107.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsThe biological unit is likely a membrane anchored monomer. However, the extracellular domain is an octamer in solution when the membrane anchor is removed.

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Components

#1: Protein SipA


Mass: 18636.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: 90/306S / Gene: sipA / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R9TES9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M NaKPO4 pH 7.0, 8% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95468 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2011 / Details: Adaptive and mechanically bent Si mirrors
RadiationMonochromator: Si111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95468 Å / Relative weight: 1
ReflectionResolution: 2.2→28.75 Å / Num. all: 28860 / Num. obs: 28860 / % possible obs: 99.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.7 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 28.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.2-2.3141.43.6551.340063.797.5
6.94-28.7538.10.03107.510430.03198.7
4.91-6.9441.20.04191.217590.042100
4.01-4.9140.40.04789.422300.047100
3.47-4.01420.08154.525920.082100
3.11-3.4743.10.14332.629100.145100
2.83-3.1143.70.2891732060.293100
2.62-2.8343.80.6967.534600.704100
2.46-2.62441.2894.137181.303100
2.31-2.4644.12.1352.439362.16100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8W

4k8w


Resolution: 2.2→28.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.626 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22933 1487 5.2 %RANDOM
Rwork0.20089 ---
obs0.20231 27299 99.38 %-
all-27470 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.584 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 49 75 2282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022256
X-RAY DIFFRACTIONr_bond_other_d0.0030.021526
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9923065
X-RAY DIFFRACTIONr_angle_other_deg0.7823.0113713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.085274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35923.16398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05315340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0531515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02460
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 105 -
Rwork0.419 1655 -
obs-1655 92.83 %

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