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- PDB-5kkd: Truncated hemolysin A Y134A from P. mirabilis at 2.1 Angstroms re... -

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Basic information

Entry
Database: PDB / ID: 5kkd
TitleTruncated hemolysin A Y134A from P. mirabilis at 2.1 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: 2.13 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 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Structure summary / Category: entity / Item: _entity.pdbx_mutation
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8703
Polymers50,7742
Non-polymers961
Water2,918162
1
A: Hemolysin
B: Hemolysin
hetero molecules

A: Hemolysin
B: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7406
Polymers101,5484
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7660 Å2
ΔGint-51 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.080, 69.080, 234.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hemolysin


Mass: 25387.025 Da / Num. of mol.: 2 / Mutation: Y134A
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1M LiSO4, 2% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 33020 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.129 / Net I/av σ(I): 31.958 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.13-2.1720.10.7881100
2.17-2.2121.80.6911100
2.21-2.2522.80.581100
2.25-2.2923.50.561100
2.29-2.34240.5271100
2.34-2.4240.4491100
2.4-2.4624.10.3991100
2.46-2.5324.20.3641100
2.53-2.624.10.3091100
2.6-2.6824.10.2551100
2.68-2.78240.2111100
2.78-2.89240.1881100
2.89-3.0224.30.1541100
3.02-3.1824.30.1271100
3.18-3.3824.60.1081100
3.38-3.6424.90.1041100
3.64-4.0125.60.1131100
4.01-4.59260.1071100
4.59-5.7826.40.081199.9
5.78-5025.20.056199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→47.82 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.1951 1650 5.01 %
Rwork0.1701 --
obs0.1714 32913 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.43 Å2 / Biso mean: 44.53 Å2 / Biso min: 20.42 Å2
Refinement stepCycle: final / Resolution: 2.13→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 5 162 3117
Biso mean--69.1 47.39 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073022
X-RAY DIFFRACTIONf_angle_d0.8184124
X-RAY DIFFRACTIONf_chiral_restr0.06481
X-RAY DIFFRACTIONf_plane_restr0.005565
X-RAY DIFFRACTIONf_dihedral_angle_d14.3691789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1278-2.19040.24951500.21772483263399
2.1904-2.26110.25121500.190925242674100
2.2611-2.34190.23681380.198825652703100
2.3419-2.43570.23681290.186925412670100
2.4357-2.54650.20291120.189426162728100
2.5465-2.68080.21351260.186825712697100
2.6808-2.84870.25231280.189225862714100
2.8487-3.06860.20921380.185925982736100
3.0686-3.37740.19411470.164326022749100
3.3774-3.86590.1621490.157726342783100
3.8659-4.86990.16711340.140126862820100
4.8699-47.83220.18361490.172528573006100
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)
16.95890.60021.35468.2018-0.59756.3617-0.1941-0.00780.66650.32360.05930.5977-1.2421-0.21290.28340.8307-0.0021-0.03210.2690.03340.44518.945344.2154-8.8551
25.7723-1.0171.31972.4802-0.91284.2584-0.2755-0.34850.4472-0.06890.05770.2592-0.9286-0.38960.18740.62550.1262-0.09290.26040.010.42843.149738.1971-7.7764
33.72731.9858-0.92263.8686-0.15263.30530.1164-0.31410.39660.4422-0.06620.0538-1.2165-0.2476-0.08470.71830.075-0.12290.2631-0.02670.34938.555738.62821.771
45.4178-0.6345-0.71813.8005-1.50933.8145-0.2050.2070.6204-0.31370.1587-0.1408-0.6669-0.1833-0.00120.5006-0.0286-0.08090.1906-0.00610.31699.572934.3726-15.7577
51.8555-0.2038-1.28151.46340.37655.9597-0.1039-0.15350.15630.1371-0.0111-0.1217-0.486-0.04860.06850.3701-0.0287-0.07010.20030.02970.289110.525828.6977-7.9281
66.189-2.97551.81571.9228-0.22344.8297-0.05510.53661.24530.2487-0.08410.3954-1.0086-1.40090.10920.41950.1566-0.02230.51610.00130.5461-5.398529.007-15.8612
75.2456-0.67783.01372.4261-0.36148.1807-0.02690.0759-0.03210.03130.0167-0.0935-0.15760.11990.00610.2383-0.0508-0.01370.13080.02970.240313.159120.5693-15.2165
84.6004-0.0654-0.16114.39391.44942.1889-0.1016-0.2493-0.2330.1425-0.10410.26140.2904-0.42660.23090.2902-0.0186-0.02290.37490.06610.3172-0.912418.1685-20.7566
95.9656-0.20282.37173.50061.98013.6866-0.11380.3464-1.0873-0.420.16290.16220.94580.4598-0.13010.82610.17680.0380.333-0.00450.566223.484-12.7287-15.5685
103.25990.23431.05023.8289-0.89162.3917-0.0339-0.1467-0.8925-0.030.08760.02841.07240.3937-0.10840.72960.1680.08540.28550.06110.526722.4263-10.9533-9.7521
112.6734-0.0803-0.06262.6364-0.27243.6697-0.01850.0792-0.281-0.161-0.0199-0.03950.53110.30480.01170.31530.00680.01470.2330.00630.250520.21863.1098-16.7384
126.8226-0.9873-4.29063.57063.06366.32710.0373-0.5651-0.02420.07450.074-0.2646-0.07391.0103-0.07790.272-0.01390.00110.4223-0.00620.278328.205913.8971-19.5443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 49 )A31 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 71 )A50 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 107 )A72 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 123 )A108 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 159 )A124 - 159
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 173 )A160 - 173
7X-RAY DIFFRACTION7chain 'A' and (resid 174 through 216 )A174 - 216
8X-RAY DIFFRACTION8chain 'A' and (resid 217 through 234 )A217 - 234
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 62 )B30 - 62
10X-RAY DIFFRACTION10chain 'B' and (resid 63 through 107 )B63 - 107
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 210 )B108 - 210
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 233 )B211 - 233

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