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- PDB-1t2o: Crystal structure of Se-SrtA, C184-Ala -

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Basic information

Entry
Database: PDB / ID: 1t2o
TitleCrystal structure of Se-SrtA, C184-Ala
Componentssortase
KeywordsHYDROLASE / Sortase / BETA BARREL / Transpeptidase
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / ion binding / 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 / SYNCHROTRON / SAD / Resolution: 2.3 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
B: sortase
C: sortase


Theoretical massNumber of molelcules
Total (without water)49,6663
Polymers49,6663
Non-polymers00
Water95553
1
A: sortase


Theoretical massNumber of molelcules
Total (without water)16,5551
Polymers16,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: sortase


Theoretical massNumber of molelcules
Total (without water)16,5551
Polymers16,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: sortase


Theoretical massNumber of molelcules
Total (without water)16,5551
Polymers16,5551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.553, 82.407, 56.112
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein sortase /


Mass: 16555.402 Da / Num. of mol.: 3 / Fragment: Delta-N59 (residues 61-206) / Mutation: C184A
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 / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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 % / Description: THE FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 300 K / 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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791, 0.9439, 1.212
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2002
RadiationMonochromator: NI MIRROR + NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.94391
31.2121
ReflectionResolution: 2.3→2.4 Å / Num. obs: 35415 / % possible obs: 99 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.2 Å2
Reflection shellResolution: 2.3→2.4 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→17.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1604167.94 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: THE FILE CONTAINS FRIEDEL PAIRS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3413 9.6 %RANDOM
Rwork0.221 ---
obs0.221 35415 98.7 %-
all-8609 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.53 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-2.45 Å2
2---4.25 Å20 Å2
3---4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→17.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 53 3425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 562 9.6 %
Rwork0.274 5293 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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