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- PDB-5kf3: Truncated hemolysin A from P. mirabilis Y134A at 2.2 Angstroms re... -

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Basic information

Entry
Database: PDB / ID: 5kf3
TitleTruncated hemolysin A from P. mirabilis Y134A at 2.2 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
Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Hemagglutinin repeat / Hemagglutinin repeat / 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: 2.2 Å
AuthorsNovak, W.R.P. / Bhattacharyya, B. / 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
DepositionJun 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)25,3871
Polymers25,3871
Non-polymers00
Water2,972165
1
A: Hemolysin

A: Hemolysin


Theoretical massNumber of molelcules
Total (without water)50,7742
Polymers50,7742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557x,-y,-z+21
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.906, 59.775, 115.766
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: 25387.025 Da / Num. of mol.: 1
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 / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 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: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12612 / % possible obs: 99.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.094 / Net I/av σ(I): 23 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.247.50.207198.4
2.24-2.288.40.214199.7
2.28-2.328.40.2071100
2.32-2.378.40.198199.7
2.37-2.428.40.203199.5
2.42-2.488.60.207199.3
2.48-2.548.40.1921100
2.54-2.618.50.181199.7
2.61-2.698.60.168199.8
2.69-2.778.40.151199.7
2.77-2.878.60.146199.8
2.87-2.998.80.133199.8
2.99-3.128.90.121100
3.12-3.299.30.1021100
3.29-3.499.40.0831100
3.49-3.769.70.0771100
3.76-4.1410.10.0651100
4.14-4.749.50.0571100
4.74-5.979.70.061100
5.97-508.90.057199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.36 Å32.54 Å
Translation6.36 Å32.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4w8q

4w8q


Resolution: 2.2→32.539 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.47
RfactorNum. reflection% reflection
Rfree0.2069 632 5.04 %
Rwork0.1727 --
obs0.1744 12528 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.22 Å2 / Biso mean: 23.0421 Å2 / Biso min: 6.26 Å2
Refinement stepCycle: final / Resolution: 2.2→32.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 0 165 1884
Biso mean---33.05 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041753
X-RAY DIFFRACTIONf_angle_d0.6412382
X-RAY DIFFRACTIONf_chiral_restr0.048273
X-RAY DIFFRACTIONf_plane_restr0.004325
X-RAY DIFFRACTIONf_dihedral_angle_d12.5991042
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.36990.2361330.17412318245199
2.3699-2.60840.25831220.195323322454100
2.6084-2.98560.21941330.189523422475100
2.9856-3.76060.19021160.159624022518100
3.7606-32.54260.18251280.16625022630100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.70770.0245-0.14940.1230.11090.5144-0.0212-0.0689-0.10090.234-0.0087-0.0098-0.3895-0.1065-0.03050.15320.0255-0.02470.1212-0.01310.111345.825719.5661145.3681
20.32940.3518-0.16570.590.38780.3827-0.0821-0.0511-0.0181-0.12850.05520.002-0.0885-0.0367-0.08180.08360.00380.00470.0807-0.00050.07851.127320.6324139.3266
30.11020.2268-0.0750.35940.34510.5647-0.0332-0.0817-0.0634-0.1058-0.0131-0.0759-0.025-0.0923-0.23490.0793-0.00090.01410.10870.01170.102547.094213.0935135.2998
40.30720.1136-0.35820.5446-0.16430.38770.035-0.097-0.06390.0377-0.02890.0006-0.08520.050.01250.0866-0.01640.00960.11950.0060.111349.03392.0886134.8374
50.2679-0.1532-0.03840.8072-0.43150.6056-0.00070.0351-0.0165-0.26550.0737-0.01710.11260.09840.17990.1489-0.0110.02710.12060.00010.116646.79793.8609125.6959
60.3675-0.27610.02960.333-0.13740.39160.03710.0921-0.2205-0.67250.02180.12340.3659-0.1784-0.01070.2428-0.0068-0.06390.2295-0.03720.206642.5643-4.0968124.7619
70.5509-0.1037-0.39770.373-0.01860.33560.26010.254-0.4730.08580.0834-0.13590.2312-0.0480.12220.3238-0.0326-0.09110.268-0.04760.207744.5909-4.8922120.3942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 54 )A30 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 101 )A55 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 153 )A102 - 153
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 187 )A154 - 187
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 226 )A188 - 226
6X-RAY DIFFRACTION6chain 'A' and (resid 227 through 248 )A227 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 263 )A249 - 263

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