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- PDB-3fy3: Crystal structure of truncated hemolysin A from P. mirabilis -

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Basic information

Entry
Database: PDB / ID: 3fy3
TitleCrystal structure of truncated hemolysin A from P. mirabilis
ComponentsHemolysin
KeywordsTOXIN / beta helix / hemolysin / solenoid / two partner secretion / Cell membrane / Cell outer membrane / Cytolysis / Hemolysis / Membrane
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeaver, T.M. / Thompson, J.R. / Bailey, L.J. / Wawrzyn, G.T. / Hocking, J.M. / Howard, D.R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and functional studies of truncated hemolysin A from Proteus mirabilis.
Authors: Weaver, T.M. / Hocking, J.M. / Bailey, L.J. / Wawrzyn, G.T. / Howard, D.R. / Sikkink, L.A. / Ramirez-Alvarado, M. / Thompson, J.R.
History
DepositionJan 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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 1.3Nov 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)24,6501
Polymers24,6501
Non-polymers00
Water00
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)49,3002
Polymers49,3002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.273, 119.528, 34.199
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Details1

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Components

#1: Protein Hemolysin


Mass: 24650.242 Da / Num. of mol.: 1 / Fragment: UNP residues 30-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: pLB265 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P16466
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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8 M Na/KH2PO4, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 2, 2007 / Details: Varimax optics
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→56 Å / Num. obs: 22150 / % possible obs: 100 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1rwr

1rwr


Resolution: 1.8→40.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.849 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20283 585 2.6 %RANDOM
Rwork0.1493 ---
obs0.15063 21597 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.092 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 0 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211990
X-RAY DIFFRACTIONr_bond_other_d0.0010.021741
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9482728
X-RAY DIFFRACTIONr_angle_other_deg0.84434096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.7825.85194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.169158
X-RAY DIFFRACTIONr_chiral_restr0.1130.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022391
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02393
X-RAY DIFFRACTIONr_nbd_refined0.1980.2291
X-RAY DIFFRACTIONr_nbd_other0.1980.21652
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2953
X-RAY DIFFRACTIONr_nbtor_other0.0870.21280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2680.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.67451665
X-RAY DIFFRACTIONr_mcbond_other1.1695540
X-RAY DIFFRACTIONr_mcangle_it4.12562088
X-RAY DIFFRACTIONr_scbond_it4.7696772
X-RAY DIFFRACTIONr_scangle_it6.327.5635
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 32 -
Rwork0.189 1556 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 10.0922 Å / Origin y: -16.9626 Å / Origin z: -12.7039 Å
111213212223313233
T-0.1835 Å20.0134 Å20.0014 Å2--0.2036 Å20.0005 Å2---0.2013 Å2
L1.4477 °2-0.0936 °2-0.0282 °2-0.8803 °20.2304 °2--0.8898 °2
S0.0137 Å °0.0403 Å °0.1468 Å °0.0631 Å °-0.0248 Å °-0.0039 Å °0.003 Å °0.0525 Å °0.011 Å °

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