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- PDB-7koh: Crystal structure of antigen 43 from Escherichia coli EDL933 -

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Basic information

Entry
Database: PDB / ID: 7koh
TitleCrystal structure of antigen 43 from Escherichia coli EDL933
ComponentsAntigen 43
KeywordsMICROBIAL PROTEIN / Autotransporters / Biofilm / Bacterial virulence / Bacterial infection
Function / homology
Function and homology information


cell outer membrane / periplasmic space / cell surface / extracellular region
Similarity search - Function
Autochaperone Domain Type 1 / Adhesin of bacterial autotransporter system / Autochaperone domain type 1 / Adhesin of bacterial autotransporter system, probable stalk / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain ...Autochaperone Domain Type 1 / Adhesin of bacterial autotransporter system / Autochaperone domain type 1 / Adhesin of bacterial autotransporter system, probable stalk / ESPR domain / Extended Signal Peptide of Type V secretion system / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative adhesin
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsVo, J.L. / Paxman, J.J. / Heras, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)180102987 Australia
Australian Research Council (ARC)150102287 Australia
National Health and Medical Research Council (NHMRC, Australia)1143638 Australia
CitationJournal: NPJ Biofilms Microbiomes / Year: 2022
Title: Variation of Antigen 43 self-association modulates bacterial compacting within aggregates and biofilms.
Authors: Vo, J.L. / Ortiz, G.C.M. / Totsika, M. / Lo, A.W. / Hancock, S.J. / Whitten, A.E. / Hor, L. / Peters, K.M. / Ageorges, V. / Caccia, N. / Desvaux, M. / Schembri, M.A. / Paxman, J.J. / Heras, B.
History
DepositionNov 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen 43
B: Antigen 43
C: Antigen 43
D: Antigen 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,20968
Polymers228,3384
Non-polymers8,87064
Water6,071337
1
A: Antigen 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42016
Polymers57,0851
Non-polymers2,33515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antigen 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42519
Polymers57,0851
Non-polymers2,34118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Antigen 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,77612
Polymers57,0851
Non-polymers1,69211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Antigen 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,58821
Polymers57,0851
Non-polymers2,50320
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.550, 178.660, 246.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Antigen 43


Mass: 57084.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 EDL933 / Gene: Z1211, Z1651 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8X9L4

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Non-polymers , 7 types, 401 molecules

#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.72 Å3/Da / Density % sol: 73.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: 100 mM SPG (succinic acid, sodium dihydrogen phosphate and glycine) pH 7.4, 27% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.98→50.83 Å / Num. obs: 86188 / % possible obs: 97.3 % / Redundancy: 6.4 % / CC1/2: 0.94 / Rmerge(I) obs: 0.483 / Rpim(I) all: 0.197 / Rrim(I) all: 0.523 / Net I/σ(I): 4.6 / Num. measured all: 551091 / Scaling rejects: 61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.98-3.036.42.5942625141180.3171.0382.7970.992.2
16.05-50.836.10.06540096520.8530.0310.07214.297.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KO9

7ko9


Resolution: 2.98→48.78 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 4222 4.9 %
Rwork0.2058 81868 -
obs0.2081 86090 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.97 Å2 / Biso mean: 45.8778 Å2 / Biso min: 3.51 Å2
Refinement stepCycle: final / Resolution: 2.98→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15465 0 387 337 16189
Biso mean--58.28 32.78 -
Num. residues----2176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115932
X-RAY DIFFRACTIONf_angle_d1.18321473
X-RAY DIFFRACTIONf_dihedral_angle_d13.9082424
X-RAY DIFFRACTIONf_chiral_restr0.0682500
X-RAY DIFFRACTIONf_plane_restr0.0062869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.98-3.010.31951120.31292553266592
3.01-3.050.36251450.32632548269392
3.05-3.090.38581300.31982554268493
3.09-3.130.31261410.32662569271093
3.13-3.170.33711450.31052598274394
3.17-3.210.42261230.29852568269193
3.21-3.260.32061390.29672654279395
3.26-3.30.34121180.28692622274094
3.3-3.360.32751390.26452668280795
3.36-3.410.30211490.25822633278296
3.41-3.470.32621300.23722720285096
3.47-3.530.28831410.24232669281096
3.53-3.60.2861430.23672697284097
3.6-3.670.2841540.21822703285797
3.67-3.750.29321190.20772782290198
3.75-3.840.25461440.20362727287198
3.84-3.940.25491540.19622748290299
3.94-4.040.22711180.18752782290099
4.04-4.160.23491540.17282757291199
4.16-4.30.22821500.157627812931100
4.3-4.450.21121450.140828242969100
4.45-4.630.18341550.126928052960100
4.63-4.840.14151440.124628032947100
4.84-5.090.19121360.140128232959100
5.09-5.410.22451470.170428252972100
5.41-5.830.21241300.184628282958100
5.83-6.420.23431510.19528452996100
6.42-7.340.25911490.206628733022100
7.34-9.240.25711470.20612880302799
9.24-48.780.2231700.213330293199100
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)
11.2466-0.76840.45320.7495-0.22210.0341-0.0380.0418-0.1858-0.14960.043-0.0215-0.07090.01280.00070.2066-0.02080.05430.2671-0.02950.284663.2859-30.40365.3808
20.53660.11560.12760.46740.28130.9491-0.15720.05980.04280.02540.01890.03630.0294-0.112200.263-0.0912-0.05190.377-0.01370.21119.9597-9.4553-20.8032
30.0447-0.13730.03530.1825-0.04630.12990.1318-0.4153-0.0990.7056-0.0228-0.37780.4028-0.1251-0.00130.70140.0611-0.22580.31750.00280.54850.4943-27.443470.4654
40.3755-0.113-0.15940.3072-0.53530.56080.0381-0.1082-0.0135-0.0393-0.1035-0.22230.0689-0.0506-00.3927-0.0235-0.07370.1387-0.00190.285543.5016-18.788157.3385
50.2986-0.16560.36940.5061-0.12290.13460.0256-0.1050.1089-0.0568-0.0642-0.10080.0978-0.094-00.29660.03320.00520.2178-0.03390.233932.1936-2.774841.6401
60.73120.04470.46960.06910.20560.4174-0.178-0.07460.0745-0.1606-0.08810.0692-0.3961-0.1255-00.38690.0564-0.10180.3191-0.04430.283511.74571.441617.7893
70.37790.33350.23540.42420.35840.1447-0.18510.0595-0.05940.0826-0.01710.0907-0.1309-0.1172-00.22450.0572-0.00530.3767-0.09780.2957-2.9081-17.82831.8168
80.1608-0.0247-0.08580.23620.02270.0063-0.46820.3271-0.505-0.72340.47210.19690.00390.28190.00330.3371-0.03950.07180.4521-0.08020.3958-2.4072-25.9036-3.848
90.61940.01060.75991.59071.20922.0657-0.06790.1844-0.09680.06090.2909-0.26830.61250.04610.45030.6456-0.08940.04980.32760.08710.557141.1344-49.343541.3023
100.0982-0.1527-0.09640.7338-0.42830.08280.0169-0.1379-0.0859-0.0041-0.0059-0.07010.0199-0.0139-00.307-0.01360.02780.20690.02350.273247.2423-33.952936.7342
11-0.10130.12990.06160.66-0.06070.2885-0.0620.0964-0.0111-0.0220.10760.0526-0.11850.026400.2445-0.05630.00210.273-0.00120.241761.2772-8.428424.787
120.08190.52880.3080.4545-0.16940.2338-0.1880.09580.2012-0.20570.1244-0.013-0.0410.104400.2933-0.1147-0.01010.4351-0.02860.318181.739813.909335.6069
130.59270.02280.18070.29150.06180.6106-0.1147-0.202-0.00030.09530.0563-0.0056-0.25890.07100.2135-0.0282-0.00520.3629-0.08120.291291.540420.063657.1301
140.102-0.020.11650.0776-0.26840.44960.0094-0.0438-0.02920.2084-0.0050.0002-0.0307-0.175-00.2681-0.09540.07180.3576-0.04930.28049.80062.299880.2546
150.06120.0503-0.03710.2498-0.22570.38710.1110.0584-0.02430.0621-0.1399-0.0043-0.123-0.0251-0.00010.275-0.0287-0.00960.2184-0.00280.241524.567910.619766.8477
160.75570.257-0.00380.31650.13650.3089-0.15510.0786-0.0286-0.03580.1146-0.0444-0.0813-0.0826-00.2809-0.0298-0.01530.16920.00610.22748.694823.707747.0762
171.67350.1528-0.37280.7583-0.07211.0541-0.3745-0.19050.4567-0.1840.3070.0444-0.20310.2159-0.43260.4364-0.0351-0.17530.344-0.13410.614174.21549.512361.3065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 304 )A2 - 304
2X-RAY DIFFRACTION2chain 'A' and (resid 305 through 562 )A305 - 562
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 52 )B1 - 52
4X-RAY DIFFRACTION4chain 'B' and (resid 53 through 156 )B53 - 156
5X-RAY DIFFRACTION5chain 'B' and (resid 157 through 274 )B157 - 274
6X-RAY DIFFRACTION6chain 'B' and (resid 275 through 432 )B275 - 432
7X-RAY DIFFRACTION7chain 'B' and (resid 433 through 532 )B433 - 532
8X-RAY DIFFRACTION8chain 'B' and (resid 533 through 562 )B533 - 562
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 52 )C1 - 52
10X-RAY DIFFRACTION10chain 'C' and (resid 53 through 156 )C53 - 156
11X-RAY DIFFRACTION11chain 'C' and (resid 157 through 326 )C157 - 326
12X-RAY DIFFRACTION12chain 'C' and (resid 327 through 456 )C327 - 456
13X-RAY DIFFRACTION13chain 'C' and (resid 457 through 562 )C457 - 562
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 100 )D1 - 100
15X-RAY DIFFRACTION15chain 'D' and (resid 101 through 185 )D101 - 185
16X-RAY DIFFRACTION16chain 'D' and (resid 186 through 403 )D186 - 403
17X-RAY DIFFRACTION17chain 'D' and (resid 404 through 561 )D404 - 561

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