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- PDB-3fn7: Crystal structure of sortase A (Spy1154) from Streptococcus pyoge... -

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Basic information

Entry
Database: PDB / ID: 3fn7
TitleCrystal structure of sortase A (Spy1154) from Streptococcus pyogenes serotype M1 strain SF370
ComponentsSortase A
KeywordsHYDROLASE / sortase-fold
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis / metal ion binding
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBanfield, M.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of Streptococcus pyogenes Sortase A: Implications for Sortase mechanism
Authors: Race, P.R. / Bentley, M.L. / Melvin, J.A. / Crow, A. / Hughes, R.K. / Smith, W.D. / Sessions, R.B. / Kehoe, M.A. / McCafferty, D.G. / Banfield, M.J.
History
DepositionDec 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase A


Theoretical massNumber of molelcules
Total (without water)20,4801
Polymers20,4801
Non-polymers00
Water1,946108
1
A: Sortase A

A: Sortase A


Theoretical massNumber of molelcules
Total (without water)40,9602
Polymers40,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1600 Å2
ΔGint-11 kcal/mol
Surface area14740 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.030, 69.890, 40.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Sortase A


Mass: 20480.186 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Strain: serotype M1 strain SF370 / Gene: M5005_Spy0875, Spy1154, SPy_1154 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q99ZN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Tris (pH 6 - 7), 20 30 % (w/v) polyethyleneglycol (PEG) 8000 and 200 mM sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2007 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→29.85 Å / Num. all: 21140 / Num. obs: 21140 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 25.6 Å2 / Rsym value: 0.058 / Net I/σ(I): 27.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 3039 / Rsym value: 0.379 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FN6

3fn6


Resolution: 1.75→29.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.277 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23891 967 5 %RANDOM
Rwork0.19638 ---
all0.19846 18391 --
obs0.19846 18391 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.552 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2---1.2 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 0 108 1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221440
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9691967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8726.10259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79415244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.03153
X-RAY DIFFRACTIONr_chiral_restr0.1070.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211081
X-RAY DIFFRACTIONr_mcbond_it1.41.5929
X-RAY DIFFRACTIONr_mcangle_it2.19221510
X-RAY DIFFRACTIONr_scbond_it3.1643511
X-RAY DIFFRACTIONr_scangle_it4.5184.5451
X-RAY DIFFRACTIONr_rigid_bond_restr2.14531440
X-RAY DIFFRACTIONr_sphericity_free7.3063108
X-RAY DIFFRACTIONr_sphericity_bonded4.89731411
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 55 -
Rwork0.224 1350 -
obs--100 %

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