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- PDB-3fn6: Crystal structure of sortase A from Streptococcus pyogenes seroty... -

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Basic information

Entry
Database: PDB / ID: 3fn6
TitleCrystal structure of sortase A from Streptococcus pyogenes serotype M1 strain SF370 with the active site Cys in its sulphenic acid form
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: 1.9 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 ...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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase A


Theoretical massNumber of molelcules
Total (without water)20,4961
Polymers20,4961
Non-polymers00
Water2,864159
1
A: Sortase A

A: Sortase A


Theoretical massNumber of molelcules
Total (without water)40,9922
Polymers40,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1760 Å2
ΔGint-10 kcal/mol
Surface area14830 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.951, 69.799, 39.867
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: 20496.186 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 strian 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.: 159 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
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
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→26.26 Å / Num. all: 15111 / Num. obs: 15111 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.064 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 2170 / Rsym value: 0.258 / % 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 1T2P

1t2p


Resolution: 1.9→26.26 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.125 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22728 761 5 %RANDOM
Rwork0.18743 ---
all0.1894 14325 --
obs0.1894 14325 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2---0.86 Å20 Å2
3---2.75 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 0 159 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221370
X-RAY DIFFRACTIONr_bond_other_d0.0020.02893
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9761864
X-RAY DIFFRACTIONr_angle_other_deg0.932212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24125.71456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.519154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
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_it0.9931.5877
X-RAY DIFFRACTIONr_mcbond_other0.2451.5362
X-RAY DIFFRACTIONr_mcangle_it1.74521423
X-RAY DIFFRACTIONr_scbond_it2.4813493
X-RAY DIFFRACTIONr_scangle_it4.0234.5437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 62 -
Rwork0.213 1028 -
obs--100 %

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