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- PDB-5dv0: Structure of S. pneumoniae D39 sortase A -

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Basic information

Entry
Database: PDB / ID: 5dv0
TitleStructure of S. pneumoniae D39 sortase A
ComponentsSortase SrtA
KeywordsHYDROLASE / Sortase
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Sortase SrtA / Sortase
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.299 Å
AuthorsDeng, X.
CitationJournal: To Be Published
Title: Structure of S. pneumoniae D39 Sortase A
Authors: Deng, X.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sortase SrtA


Theoretical massNumber of molelcules
Total (without water)19,1921
Polymers19,1921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13470 Å2
2
A: Sortase SrtA

A: Sortase SrtA


Theoretical massNumber of molelcules
Total (without water)38,3832
Polymers38,3832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_466y-1,x+1,-z+11
Buried area10710 Å2
ΔGint-61 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.578, 117.578, 101.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Sortase SrtA


Mass: 19191.707 Da / Num. of mol.: 1 / Fragment: UNP residues 82-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: srtA, ERS021047_00305 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U0ITY4, UniProt: Q8DPM3*PLUS

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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: 4.61 Å3/Da / Density % sol: 73.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: (NH4)2SO4, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 5602 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 48.9
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.73 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8L

4o8l


Resolution: 3.299→38.508 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 257 4.59 %
Rwork0.24 --
obs0.2413 5600 99.38 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.066 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6702 Å20 Å20 Å2
2--4.6702 Å20 Å2
3----9.3405 Å2
Refinement stepCycle: LAST / Resolution: 3.299→38.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 0 0 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031351
X-RAY DIFFRACTIONf_angle_d0.7881825
X-RAY DIFFRACTIONf_dihedral_angle_d15.493506
X-RAY DIFFRACTIONf_chiral_restr0.031207
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.299-4.15560.33541200.28222619X-RAY DIFFRACTION100
4.1556-38.51030.2651370.22782724X-RAY DIFFRACTION99

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