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- PDB-1t2p: Crystal structure of Sortase A from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 1t2p
TitleCrystal structure of Sortase A from Staphylococcus aureus
Componentssortase
KeywordsHYDROLASE / Sortase / BETA BARREL / transpeptidase
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / peptide binding / manganese ion binding / calcium ion binding / magnesium ion binding / proteolysis
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 speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: CRYSTAL STRUCTURES OF STAPHYLOCOCCUS AUREUS SORTASE A AND ITS SUBSTRATE COMPLEX
Authors: Zong, Y. / Bice, T.W. / Ton-That, H. / Schneewind, O. / Narayana, S.V.
History
DepositionApr 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sortase
B: sortase
C: sortase


Theoretical massNumber of molelcules
Total (without water)49,4813
Polymers49,4813
Non-polymers00
Water6,521362
1
A: sortase


Theoretical massNumber of molelcules
Total (without water)16,4941
Polymers16,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sortase


Theoretical massNumber of molelcules
Total (without water)16,4941
Polymers16,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: sortase


Theoretical massNumber of molelcules
Total (without water)16,4941
Polymers16,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.553, 81.907, 54.912
Angle α, β, γ (deg.)90.00, 103.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein sortase


Mass: 16493.676 Da / Num. of mol.: 3 / Fragment: Delta-N59 (residues 61-206)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: srt / Plasmid: Novagen pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q9S446
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 1.9 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.35
Details: Ammonium Sulfate, MES, Sodium Chloride, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2002 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→1.85 Å / Num. all: 34566 / Num. obs: 33894 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 10 Å2
Reflection shellResolution: 1.75→1.85 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2O

1t2o


Resolution: 2→35.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 385696.14 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2566 9.9 %RANDOM
Rwork0.209 ---
all0.221 33211 --
obs0.209 25810 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.9362 Å2 / ksol: 0.37371 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å2-1.06 Å2
2---3.24 Å20 Å2
3----0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 0 362 3759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 375 9.5 %
Rwork0.209 3564 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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