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- PDB-4w8t: Crystal structure of truncated hemolysin A Q125S from P. mirabili... -

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Basic information

Entry
Database: PDB / ID: 4w8t
TitleCrystal structure of truncated hemolysin A Q125S from P. mirabilis at 1.5 Angstroms resolution
ComponentsHemolysin
KeywordsTOXIN / hemolysin / two partner secretion / beta solenoid / beta helix
Function / homology
Function and homology information


catalytic activity / cell outer membrane / toxin activity / killing of cells of another organism
Similarity search - Function
Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemagglutinin repeat / Hemagglutinin repeat / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.539 Å
AuthorsNovak, W.R.P. / Glasgow, E. / Thompson, J.R. / Weaver, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1050435 United States
CitationJournal: To Be Published
Title: Crystal structure of truncated hemolysin A Q125S from P. mirabilis at 1.5 Angstroms resolution
Authors: Novak, W.R.P. / Glasgow, E. / Thompson, J.R. / Weaver, T.M.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_mutation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 21, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Hemolysin


Theoretical massNumber of molelcules
Total (without water)25,4381
Polymers25,4381
Non-polymers00
Water4,630257
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)50,8762
Polymers50,8762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.593, 34.156, 67.597
Angle α, β, γ (deg.)90.00, 99.02, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-339-

HOH

31A-390-

HOH

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Components

#1: Protein Hemolysin /


Mass: 25438.072 Da / Num. of mol.: 1 / Mutation: Q125S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / References: UniProt: P16466
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM citrate pH 5.5, 100 mM NaCl, PEG 4000 (8 - 16%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.539→25.5 Å / Num. obs: 40088 / % possible obs: 99.7 % / Redundancy: 6.7 % / Net I/σ(I): 15.8
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 1.539→25.493 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 1943 5.05 %Random
Rwork0.1674 ---
obs0.1685 38500 95.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.539→25.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 0 257 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081775
X-RAY DIFFRACTIONf_angle_d1.1562413
X-RAY DIFFRACTIONf_dihedral_angle_d11.328634
X-RAY DIFFRACTIONf_chiral_restr0.048275
X-RAY DIFFRACTIONf_plane_restr0.006330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5386-1.57710.27551210.2532209X-RAY DIFFRACTION82
1.5771-1.61970.26981350.22682439X-RAY DIFFRACTION90
1.6197-1.66730.22051330.21552411X-RAY DIFFRACTION90
1.6673-1.72110.25721400.21332543X-RAY DIFFRACTION93
1.7211-1.78260.23081320.1992547X-RAY DIFFRACTION94
1.7826-1.8540.22971370.18792620X-RAY DIFFRACTION96
1.854-1.93840.21291380.18132618X-RAY DIFFRACTION96
1.9384-2.04050.18611390.17032672X-RAY DIFFRACTION98
2.0405-2.16830.19611410.17172681X-RAY DIFFRACTION99
2.1683-2.33560.20011430.16642698X-RAY DIFFRACTION99
2.3356-2.57040.18971430.18152727X-RAY DIFFRACTION99
2.5704-2.94190.17851450.17572758X-RAY DIFFRACTION100
2.9419-3.70470.18411460.1462785X-RAY DIFFRACTION100
3.7047-25.49690.15161500.14242849X-RAY DIFFRACTION100

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