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- PDB-6pyk: P. mirabilis hemolysin A mutant - F80L -

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Basic information

Entry
Database: PDB / ID: 6pyk
TitleP. mirabilis hemolysin A mutant - F80L
ComponentsHemolysin
KeywordsTOXIN / hemolysin / two-partner secretion / beta-helix / protein secretion
Function / homology
Function and homology information


catalytic activity / cell outer membrane / toxin activity / killing of cells of another organism
Similarity search - Function
Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWeaver, T.M. / Novak, W.R.P. / Bhattacharyya, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1050435 United States
National Science Foundation (NSF, United States)REU1434473 United States
CitationJournal: To Be Published
Title: Structure of truncated hemolysin A variant F80L
Authors: Weaver, T.M. / Novak, W.R.P. / Bhattacharyya, B. / Woods, C.N. / Grilley, D.P. / Wimmer, M.R.
History
DepositionJul 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)25,4451
Polymers25,4451
Non-polymers00
Water2,144119
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)50,8902
Polymers50,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_754-x+2,y,-z-11
Buried area1650 Å2
ΔGint-8 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 34.011, 59.480
Angle α, β, γ (deg.)90.000, 101.020, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Hemolysin


Mass: 25445.107 Da / Num. of mol.: 1 / Mutation: F80L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: pET24a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 20, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Double crystal cry-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→34.011 Å / Num. obs: 44578 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Net I/σ(I): 15.9
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4273 / Rpim(I) all: 0.331 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FY3

3fy3


Resolution: 1.35→34.011 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.32
RfactorNum. reflection% reflection
Rfree0.1615 2172 4.87 %
Rwork0.133 --
obs0.1344 44567 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.78 Å2 / Biso mean: 21.3845 Å2 / Biso min: 8.62 Å2
Refinement stepCycle: final / Resolution: 1.35→34.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 119 1901
Biso mean---36.85 -
Num. residues----241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3501-1.37950.23681400.1828242093
1.3795-1.41160.22331490.1643264999
1.4116-1.44690.21811200.15612632100
1.4469-1.4860.21340.13182668100
1.486-1.52970.16131290.11832645100
1.5297-1.57910.15571330.10292636100
1.5791-1.63550.1561390.09982656100
1.6355-1.7010.16541390.10312672100
1.701-1.77840.1581280.10652668100
1.7784-1.87220.14981460.10352644100
1.8722-1.98940.16331380.10292644100
1.9894-2.1430.13781240.112704100
2.143-2.35860.13721410.12022656100
2.3586-2.69980.16041330.14732679100
2.6998-3.4010.17121490.14662704100
3.401-34.0110.15841300.1578271897

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