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- PDB-4e1s: X-ray crystal structure of the transmembrane beta-domain from int... -

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Basic information

Entry
Database: PDB / ID: 4e1s
TitleX-ray crystal structure of the transmembrane beta-domain from intimin from EHEC strain O157:H7
ComponentsIntimin
KeywordsCELL ADHESION / outer membrane beta barrel / adhesin / translocated intimin receptor
Function / homology
Function and homology information


cell outer membrane / cell adhesion
Similarity search - Function
Inverse autotransporter, beta-domain / Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain ...Inverse autotransporter, beta-domain / Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Porin / C-type lectin-like/link domain superfamily / C-type lectin fold / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Intimin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD / molecular replacement / Resolution: 1.855 Å
AuthorsFairman, J.W. / Dautin, N. / Wojtowicz, D. / Wei, L. / Noinaj, N. / Barnard, T.J. / Udho, E. / Finkelstein, A. / Przytycka, T.M. / Cherezov, V. / Buchanan, S.K.
CitationJournal: Structure / Year: 2012
Title: Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis.
Authors: Fairman, J.W. / Dautin, N. / Wojtowicz, D. / Liu, W. / Noinaj, N. / Barnard, T.J. / Udho, E. / Przytycka, T.M. / Cherezov, V. / Buchanan, S.K.
History
DepositionMar 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,45715
Polymers27,7871
Non-polymers4,67014
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.565, 120.248, 39.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

OLC

21A-679-

HOH

31A-737-

HOH

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Components

#1: Protein Intimin / / Attaching and effacing protein / Eae protein / Gamma-intimin


Mass: 27786.594 Da / Num. of mol.: 1 / Fragment: transmembrane domain (UNP residues 208-449)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EHEC O157:H7 / Gene: eae, eaeA, ECs4559, Intimin, L0025, Z5110 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43261
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase monoolein / pH: 4.5
Details: 0.1 M sodium citrate, pH 4.5-5.5, 0.05-0.1 M sodium chloride, 0.1-0.15 M magnesium chloride, 30-34% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.034375
SYNCHROTRONAPS 23-ID-B20.98069,0.95044,0.98047
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDDec 17, 2010K-B pair of biomorph mirrors
MARMOSAIC 300 mm CCD2CCDMar 23, 2011K-B pair of biomorph mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0343751
20.980691
30.950441
40.980471
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 21.07 / Number: 43035 / Rmerge(I) obs: 0.102 / Χ2: 1.01 / D res high: 2.74 Å / D res low: 50 Å / Num. obs: 12313 / % possible obs: 88.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.95099.610.0591.0123.8
4.685.910010.0761.0213.9
4.094.6810010.071.0163.9
3.724.0910010.111.0373.9
3.453.7210010.1231.0153.8
3.253.4599.410.1681.0173.6
3.093.2593.210.1870.9943.3
2.953.0979.910.2531.0042.8
2.842.9561.610.2540.992.6
2.742.8449.210.2470.9952.3
ReflectionResolution: 1.85→50 Å / Num. all: 23801 / Num. obs: 22224 / % possible obs: 93.6 % / Observed criterion σ(F): 1.85 / Observed criterion σ(I): 1.85 / Redundancy: 5.1 % / Rmerge(I) obs: 0.088 / Χ2: 1.518 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.90.57816481.0171,271.5
1.92-1.994.20.4819851.0361,285
1.99-2.084.50.39821971.0951,293.1
2.08-2.194.80.29722841.1111,297.2
2.19-2.335.20.24823111.1921,298.9
2.33-2.515.50.19723481.3161,299.7
2.51-2.765.70.14123621.3911,299.6
2.76-3.165.70.09123861.5511,299.7
3.16-3.995.50.0624102.481,299.9
3.99-5050.04322932.3811,290.6

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
SHARPphasing
SOLOMONphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT / Resolution: 1.855→27.899 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.804 / SU ML: 0.48 / σ(F): 0 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1152 5.19 %RANDOM
Rwork0.175 ---
all0.1779 23801 --
obs0.1779 22197 93.26 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.248 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 112.63 Å2 / Biso mean: 32.0012 Å2 / Biso min: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1-22.9519 Å2-0 Å2-0 Å2
2---0.0277 Å2-0 Å2
3----3.9726 Å2
Refinement stepCycle: LAST / Resolution: 1.855→27.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 313 163 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062365
X-RAY DIFFRACTIONf_angle_d1.1433119
X-RAY DIFFRACTIONf_chiral_restr0.08291
X-RAY DIFFRACTIONf_plane_restr0.004404
X-RAY DIFFRACTIONf_dihedral_angle_d25.568985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.855-1.93940.36381120.27771956206871
1.9394-2.04160.2871280.23992472260088
2.0416-2.16950.24941460.19872664281096
2.1695-2.33690.24421620.18532748291099
2.3369-2.5720.23071430.173728012944100
2.572-2.94380.23871740.166527752949100
2.9438-3.70750.1981590.138928423001100
3.7075-27.90170.22181280.1742787291593
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)
16.35571.9661-3.62713.459-0.96897.01890.44230.03721.0855-0.12910.40060.226-0.7461-0.5875-0.1906-0.18040.23580.0989-0.0887-0.04430.0777-27.3712-24.26835.8998
23.13511.7272-1.31962.7507-0.4062.69040.28250.16370.38160.2007-0.0630.1785-0.3442-0.0862-0.15920.1941-0.0070.0010.09860.0150.1802-23.6948-18.80850.0867
32.30770.66030.05473.03180.21172.3036-0.25280.05080.15930.16660.08970.4079-0.3294-0.5608-0.02080.0852-0.09370.0233-0.07390.00010.0777-28.9867-18.1283-0.2706
42.87731.6342-0.90972.4121-0.56590.89350.7125-0.0169-0.36780.5403-0.4711-0.3325-0.3484-0.0368-0.10130.2023-0.1316-0.03210.03290.02580.1025-26.8451-13.34-0.1963
53.22471.61080.04341.73810.30291.75450.0792-0.03410.00990.1819-0.0388-0.0877-0.26290.0446-0.02920.2484-0.00570.01980.12140.0120.1322-29.6932-10.9298-0.9417
64.71050.77041.24911.8323-0.04791.826-0.00190.13770.55240.3483-0.14060.144-0.3220.13240.12770.226-0.0183-0.00040.0545-0.00320.0985-29.8936-8.90172.9728
71.4833-0.48261.03451.2711-0.57772.6781-0.34410.13690.1230.17110.13960.1501-0.6371-0.04720.1080.1497-0.00970.0770.04650.00040.0936-37.7216-9.98742.7168
81.0194-0.79190.90392.0625-0.97713.45740.0912-0.31870.01340.16070.0210.2429-0.4022-0.3380.02250.093-0.07050.05970.05510.02610.1169-39.612-11.5528.079
94.1957-1.33991.14440.7058-0.14221.2998-0.073-0.43790.04430.13380.13720.0014-0.3986-0.1135-0.05750.3123-0.05230.04440.15770.01950.114-36.6172-10.371613.9218
101.3027-0.9829-0.00221.46420.18381.38710.1051-0.08050.03860.3446-0.16320.1074-0.1809-0.15610.00830.3073-0.05680.0750.17450.00790.1511-38.3661-15.778315.6031
113.0446-1.7712-0.54061.6672-0.28962.961-0.0044-0.6588-0.13630.04460.13510.0641-0.2431-0.0426-0.16310.1446-0.09150.00550.1334-0.00770.1232-34.111-19.003517.94
122.94-0.8432-1.18292.19590.65912.93670.0098-0.09220.15580.39320.00640.01520.1007-0.29820.06330.2207-0.0519-0.03320.18080.03630.1572-32.1108-22.083613.3658
130.2216-1.09620.02425.74720.72621.54220.3203-0.06230.0663-0.027-0.3162-1.1543-0.06340.47430.03990.2124-0.0698-0.03990.26020.07150.2769-12.8609-22.814411.2677
149.4640.41870.08130.4737-0.03231.62980.3073-0.3799-0.15280.1586-0.125-0.0045-0.0771-0.0262-0.180.2509-0.05210.02240.09350.02160.1518-36.6912-13.74463.7126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 208:222))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 223:238))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 239:252))A0
4X-RAY DIFFRACTION4chain 'A' and ((resseq 253:268))A0
5X-RAY DIFFRACTION5chain 'A' and ((resseq 269:283))A0
6X-RAY DIFFRACTION6chain 'A' and ((resseq 284:298))A0
7X-RAY DIFFRACTION7chain 'A' and ((resseq 299:317))A0
8X-RAY DIFFRACTION8chain 'A' and ((resseq 318:340))A0
9X-RAY DIFFRACTION9chain 'A' and ((resseq 341:360))A0
10X-RAY DIFFRACTION10chain 'A' and ((resseq 361:383))A0
11X-RAY DIFFRACTION11chain 'A' and ((resseq 384:395))A0
12X-RAY DIFFRACTION12chain 'A' and ((resseq 396:411))A0
13X-RAY DIFFRACTION13chain 'A' and ((resseq 412:434))A0
14X-RAY DIFFRACTION14chain 'A' and ((resseq 435:449))A0

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