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- PDB-4w8r: Crystal structure of hemolysin A Y134F from P. mirabilis at 1.5 A... -

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Basic information

Entry
Database: PDB / ID: 4w8r
TitleCrystal structure of hemolysin A Y134F 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
Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.519 Å
AuthorsNovak, W.R.P. / Glasgow, E. / Thompson, J.R. / Weaver, T.M.
CitationJournal: To Be Published
Title: Crystal structure of hemolysin A Y134F 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 1.1Sep 27, 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
Revision 1.2Oct 23, 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)25,4631
Polymers25,4631
Non-polymers00
Water5,008278
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)50,9262
Polymers50,9262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area1510 Å2
ΔGint-7 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.351, 119.826, 34.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hemolysin


Mass: 25463.123 Da / Num. of mol.: 1 / Mutation: Y134F
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


Mass: 18.015 Da / Num. of mol.: 278 / 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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.92 %
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: 1.519→30 Å / Num. obs: 36324 / % possible obs: 98.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 18.3
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2.5 / % possible all: 85.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FY3

3fy3


Resolution: 1.519→29.956 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
Rfree0.197 1942 5.52 %Random
Rwork0.1755 ---
obs0.1767 35192 95.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.519→29.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 278 2003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051807
X-RAY DIFFRACTIONf_angle_d0.9762458
X-RAY DIFFRACTIONf_dihedral_angle_d12.33650
X-RAY DIFFRACTIONf_chiral_restr0.039279
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5191-1.55710.30641080.2651841X-RAY DIFFRACTION75
1.5571-1.59920.27931270.23622148X-RAY DIFFRACTION90
1.5992-1.64630.22831370.20592308X-RAY DIFFRACTION94
1.6463-1.69940.2191290.2052287X-RAY DIFFRACTION94
1.6994-1.76010.22951340.19872328X-RAY DIFFRACTION96
1.7601-1.83060.22791400.18832395X-RAY DIFFRACTION98
1.8306-1.91390.19721430.18342408X-RAY DIFFRACTION98
1.9139-2.01480.2111430.17952449X-RAY DIFFRACTION99
2.0148-2.1410.19281420.17532453X-RAY DIFFRACTION99
2.141-2.30620.1951430.17142444X-RAY DIFFRACTION99
2.3062-2.53820.20961460.17732478X-RAY DIFFRACTION100
2.5382-2.90520.17621450.17952496X-RAY DIFFRACTION100
2.9052-3.65920.19541490.16282542X-RAY DIFFRACTION100
3.6592-29.96230.16541560.15162673X-RAY DIFFRACTION100

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