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- PDB-4k8w: An arm-swapped dimer of the S. pyogenes pilin specific assembly f... -

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Basic information

Entry
Database: PDB / ID: 4k8w
TitleAn arm-swapped dimer of the S. pyogenes pilin specific assembly factor SipA
ComponentsLepA
KeywordsCELL ADHESION / Predominately beta-strand / S26A signal peptidase family / pilin assembly / Extracellular membrane bound
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
ETHANOL / Signal peptidase I
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.67 Å
AuthorsYoung, P.G. / Kang, H.J. / Baker, E.N.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: An arm-swapped dimer of the Streptococcus pyogenes pilin specific assembly factor SipA.
Authors: Young, P.G. / Kang, H.J. / Baker, E.N.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: LepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7466
Polymers14,4831
Non-polymers2625
Water1,838102
1
A: LepA
hetero molecules

A: LepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,49112
Polymers28,9662
Non-polymers52510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5890 Å2
ΔGint7 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.285, 53.285, 131.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LepA


Mass: 14483.205 Da / Num. of mol.: 1 / Fragment: UNP residues 45-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: 90/306S / Gene: lepA, sipA / Plasmid: pProEXHta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RP52
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15 % ethanol, 0.10 M Tris.Cl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2009 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.67→19.31 Å / Num. all: 22923 / Num. obs: 22923 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 35.3 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.3
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 30.2 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 13.3 / Num. unique all: 3178 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXSphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.67→19.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.252 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1183 5.2 %RANDOM
Rwork0.18516 ---
all0.18662 21670 --
obs0.18662 21670 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.67→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 17 102 1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.981329
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0525121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75223.69646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24215151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.669156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021757
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.667→1.71 Å / Rfactor Rfree error: 0.081 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 68 -
Rwork0.236 1315 -
obs-1315 93.45 %

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