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- PDB-5kdk: Truncated hemolysin A from P. mirabilis at 2.0 Angstroms resoluti... -

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Basic information

Entry
Database: PDB / ID: 5kdk
TitleTruncated hemolysin A from P. mirabilis at 2.0 Angstroms resolution crystallized in a high salt condition
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 / molecular replacement / Resolution: 2.002 Å
AuthorsNovak, W.R.P. / Bhattacharyya, B. / Weaver, T.M.
CitationJournal: To Be Published
Title: Crystal structure of truncated hemolysin A from P. mirabilis at 2.0 Angstroms in high salt
Authors: Novak, W.R.P. / Bhattacharyya, B. / Grilley, D.P. / Weaver, T.M.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Oct 16, 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
Water4,216234
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_555x,-y,-z1
Buried area1470 Å2
ΔGint-9 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.440, 80.150, 96.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Hemolysin


Mass: 25479.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Production host: Escherichia coli (E. coli) / Strain (production host): pET24a+ / References: UniProt: P16466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1M LiSO4, 2% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→61.69 Å / Num. obs: 18777 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.053 / Rrim(I) all: 0.151 / Net I/σ(I): 12.5 / Num. measured all: 149045 / Scaling rejects: 118
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.057.70.4111100
8.95-61.696.20.052199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.373
Highest resolutionLowest resolution
Rotation61.69 Å2.05 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.21data scaling
MOLREPphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W8Q

4w8q


Resolution: 2.002→61.685 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.79
RfactorNum. reflection% reflection
Rfree0.1887 1008 5.38 %
Rwork0.1592 --
obs0.1608 18730 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.03 Å2 / Biso mean: 14.3059 Å2 / Biso min: 0.63 Å2
Refinement stepCycle: final / Resolution: 2.002→61.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1715 0 0 234 1949
Biso mean---25.56 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071784
X-RAY DIFFRACTIONf_angle_d0.8892431
X-RAY DIFFRACTIONf_chiral_restr0.065276
X-RAY DIFFRACTIONf_plane_restr0.005334
X-RAY DIFFRACTIONf_dihedral_angle_d14.0221061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0021-2.10770.22641410.160624622603
2.1077-2.23970.18051330.149525142647
2.2397-2.41270.18441580.152124662624
2.4127-2.65550.18951310.168225322663
2.6555-3.03970.21550.172124922647
3.0397-3.82970.19461410.155425762717
3.8297-61.71470.16641490.157726802829

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