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- PDB-6q0p: P. mirabilis hemolysin A mutant - Y134S -

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Basic information

Entry
Database: PDB / ID: 6q0p
TitleP. mirabilis hemolysin A mutant - Y134S
ComponentsHemolysin
KeywordsTOXIN / hemolysin / two-partner secretion / beta-helix / protein secretion
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 / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.542 Å
AuthorsWeaver, T.M. / Novak, W.R.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1050435 United States
National Science Foundation (NSF, United States)MCB1434473 United States
CitationJournal: To Be Published
Title: Structure of the HpmA265 Q125A variant
Authors: Weaver, T.M. / Novak, W.R.P. / Grilley, D.P. / Wimmer, M.R. / Woods, C.N. / Bhattacharyya, B.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 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)25,4031
Polymers25,4031
Non-polymers00
Water3,099172
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)50,8062
Polymers50,8062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area1660 Å2
ΔGint-7 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.742, 34.116, 68.359
Angle α, β, γ (deg.)90.000, 99.100, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

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Components

#1: Protein Hemolysin


Mass: 25403.025 Da / Num. of mol.: 1 / Mutation: Y134S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: pET24+ / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P16466
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.542→33.749 Å / Num. obs: 39365 / % possible obs: 98.3 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.039 / Net I/σ(I): 16.9
Reflection shellResolution: 1.542→1.59 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 2 / Num. unique obs: 3391 / Rpim(I) all: 0.413 / % possible all: 84.7

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W8Q

4w8q


Resolution: 1.542→33.749 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 2000 5.08 %
Rwork0.1834 37348 -
obs0.1848 39348 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.63 Å2 / Biso mean: 29.9841 Å2 / Biso min: 13.34 Å2
Refinement stepCycle: final / Resolution: 1.542→33.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 0 172 1892
Biso mean---38.97 -
Num. residues----234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.542-1.58030.24251140.2687211578
1.5803-1.62310.29751460.2452272499
1.6231-1.67080.26221420.2651266298
1.6708-1.72480.28171430.2408266698
1.7248-1.78640.25361420.2171265497
1.7864-1.85790.21871420.202265696
1.8579-1.94250.2181400.198262497
1.9425-2.04490.21621440.1964269298
2.0449-2.1730.22351430.1889266998
2.173-2.34070.20131450.1805270498
2.3407-2.57620.19611470.1955274499
2.5762-2.94880.2181480.19492766100
2.9488-3.71440.20871510.16672809100
3.7144-33.7490.19061530.1538286399

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