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- PDB-6pzl: P. mirabilis hemolysin A mutant - Q125A -

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Basic information

Entry
Database: PDB / ID: 6pzl
TitleP. mirabilis hemolysin A mutant - Q125A
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: 1.17 Å
AuthorsWeaver, T.M. / Novak, W.R.P. / Bhattacharyya, B.
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 1, 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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5142
Polymers25,4221
Non-polymers921
Water4,161231
1
A: Hemolysin
hetero molecules

A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0284
Polymers50,8442
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557x,-y,-z+21
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.047, 60.224, 116.350
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: 25422.072 Da / Num. of mol.: 1 / Mutation: Q125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16466
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 49.96 %
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: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.17→32.7 Å / Num. obs: 71123 / % possible obs: 87.2 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.012 / Net I/σ(I): 44.2
Reflection shellResolution: 1.17→1.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2859 / Rpim(I) all: 0.21

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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: 1.17→32.677 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 2000 2.82 %
Rwork0.1605 69047 -
obs0.1611 71047 87.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.12 Å2 / Biso mean: 16.588 Å2 / Biso min: 5.95 Å2
Refinement stepCycle: final / Resolution: 1.17→32.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 14 231 1944
Biso mean--38.54 28.04 -
Num. residues----230
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1704-1.19970.2913500.2388170431
1.1997-1.23210.2416830.1578288452
1.2321-1.26840.18361100.1352380368
1.2684-1.30930.16161310.1373449180
1.3093-1.35610.20981430.1417498789
1.3561-1.41040.17771600.1445549798
1.4104-1.47460.16551620.14195609100
1.4746-1.55240.18151630.13885638100
1.5524-1.64960.16921630.13275611100
1.6496-1.7770.16021650.15055671100
1.777-1.95580.16271640.15245672100
1.9558-2.23870.18111660.15465730100
2.2387-2.82030.20121670.18195767100
2.8203-32.6770.19041730.17555983100

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