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- PDB-5hu4: Cystal structure of listeria monocytogenes sortase A -

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Basic information

Entry
Database: PDB / ID: 5hu4
TitleCystal structure of listeria monocytogenes sortase A
ComponentsCysteine protease
KeywordsHYDROLASE / protease / sortase A
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / plasma membrane
Similarity search - Function
Sortase A / Sortase family / Sortase domain superfamily / Sortase domain
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, H.
CitationJournal: Biochem. Pharmacol. / Year: 2016
Title: Inhibition of sortase A by chalcone prevents Listeria monocytogenes infection.
Authors: Li, H. / Chen, Y. / Zhang, B. / Niu, X. / Song, M. / Luo, Z. / Lu, G. / Liu, B. / Zhao, X. / Wang, J. / Deng, X.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Cysteine protease


Theoretical massNumber of molelcules
Total (without water)16,1131
Polymers16,1131
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7460 Å2
Unit cell
Length a, b, c (Å)36.986, 56.599, 60.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cysteine protease / Sortase family protein


Mass: 16113.419 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 78-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: ABE86_07720, ABE87_06300, AMC92_10805, ARD00_01217 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P6T3F9, UniProt: Q8Y8H5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.97 Å3/Da / Density % sol: 37.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% w/v PEG 2000, 0.1 mol/L Tris-HCl (PH 8.5), 0.01 mol/L Ni2SO4 6H2O

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 6042 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.73 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.182 / Net I/av σ(I): 18.445 / Net I/σ(I): 11 / Num. measured all: 40438
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.386.50.3045861.42399.7
2.38-2.486.80.2535881.325100
2.48-2.596.90.2145941.254100
2.59-2.736.80.1925861.209100
2.73-2.96.80.1615941.183100
2.9-3.126.80.1195981.183100
3.12-3.446.90.0835911.165100
3.44-3.936.80.0656160.995100
3.93-4.956.60.056211.078100
4.95-506.10.056681.03198.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 2.3→22.475 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 291 4.84 %
Rwork0.2335 5719 -
obs0.2357 6010 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.25 Å2 / Biso mean: 27.3627 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 2.3→22.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 0 30 1133
Biso mean---28.9 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021113
X-RAY DIFFRACTIONf_angle_d0.6421511
X-RAY DIFFRACTIONf_chiral_restr0.026185
X-RAY DIFFRACTIONf_plane_restr0.003193
X-RAY DIFFRACTIONf_dihedral_angle_d14.842409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.380.36841260.284528102936
2.38-22.47630.24431650.211429093074

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