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- PDB-4w8q: Crystal structure of truncated hemolysin A from P. mirabilis at 1... -

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Basic information

Entry
Database: PDB / ID: 4w8q
TitleCrystal structure of truncated hemolysin A from P. mirabilis at 1.4 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 / 3 Solenoid / Pectin lyase fold / Pectin lyase fold/virulence factor / Mainly Beta
Similarity search - Domain/homology
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.428 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: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Proteolysis of truncated hemolysin A yields a stable dimerization interface.
Authors: Novak, W.R. / Bhattacharyya, B. / Grilley, D.P. / Weaver, T.M.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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 1.7Nov 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)25,4791
Polymers25,4791
Non-polymers00
Water5,062281
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)50,9582
Polymers50,9582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.719, 34.317, 68.309
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

21A-551-

HOH

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Components

#1: Protein Hemolysin


Mass: 25479.123 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: pET24a+ / Production host: Escherichia coli (E. coli) / References: UniProt: P16466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.428→29.7 Å / Num. obs: 49625 / % possible obs: 97.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 25.4
Reflection shellResolution: 1.428→1.46 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.2 / % possible all: 74.9

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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: 1.428→29.658 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1629 1936 4.03 %Random
Rwork0.1391 ---
obs0.1401 48038 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.428→29.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 281 2007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161817
X-RAY DIFFRACTIONf_angle_d1.5232476
X-RAY DIFFRACTIONf_dihedral_angle_d12.935652
X-RAY DIFFRACTIONf_chiral_restr0.083279
X-RAY DIFFRACTIONf_plane_restr0.008342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4283-1.4640.2424950.20752131X-RAY DIFFRACTION62
1.464-1.50360.20121130.17772680X-RAY DIFFRACTION77
1.5036-1.54780.20191290.14433160X-RAY DIFFRACTION91
1.5478-1.59780.16591380.12553289X-RAY DIFFRACTION95
1.5978-1.65490.15761380.12163372X-RAY DIFFRACTION96
1.6549-1.72110.16511430.12253389X-RAY DIFFRACTION97
1.7211-1.79950.14751440.12213426X-RAY DIFFRACTION98
1.7995-1.89430.13951450.12033452X-RAY DIFFRACTION99
1.8943-2.0130.15931450.11853465X-RAY DIFFRACTION99
2.013-2.16840.14671470.12773491X-RAY DIFFRACTION100
2.1684-2.38650.16131490.13413519X-RAY DIFFRACTION100
2.3865-2.73160.19821470.1563530X-RAY DIFFRACTION100
2.7316-3.44070.18711510.15143567X-RAY DIFFRACTION100
3.4407-29.66410.13921520.14043631X-RAY DIFFRACTION99

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