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- PDB-4e1t: X-ray crystal structure of the transmembrane beta-domain from inv... -

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Basic information

Entry
Database: PDB / ID: 4e1t
TitleX-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis
ComponentsInvasin
KeywordsCELL ADHESION / outer membrane beta barrel / adhesin / integrin
Function / homology
Function and homology information


cell adhesion / cell surface
Similarity search - Function
: / Invasin, domain 4 / Inverse autotransporter, beta-domain / Invasin, domain 3 / Invasin, domain 3 / Intimin, C-terminal / Intimin C-type lectin domain / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily ...: / Invasin, domain 4 / Inverse autotransporter, beta-domain / Invasin, domain 3 / Invasin, domain 3 / 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 / 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 / Invasin
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.263 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 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Invasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,49614
Polymers27,8611
Non-polymers4,63513
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.404, 124.885, 65.073
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Invasin /


Mass: 27860.967 Da / Num. of mol.: 1 / Fragment: transmembrane domain (UNP residues 147-390) / Mutation: L352F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: invasin, YPTB1668 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11922
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase monoolein / pH: 4
Details: 0.05 M sodium citrate, pH 3.8-4.4, 0.2 M lithium sulfate, 23-35% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.034375 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 24, 2011 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034375 Å / Relative weight: 1
ReflectionResolution: 2.263→67.007 Å / Num. all: 15222 / Num. obs: 14111 / % possible obs: 92.7 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.133 / Χ2: 1.008 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.263-2.382.90.59911331.058176.2
2.38-2.483.40.59312511.044183
2.48-2.594.10.56213511.033190.1
2.59-2.7350.46314231.014194.9
2.73-2.95.40.34914821.005198.7
2.9-3.125.90.28315211.003199.9
3.12-3.4460.18415141.0121100
3.44-3.9360.13415221.0211100
3.93-4.955.40.09213000.986183.8
4.95-505.70.09516140.966199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E1S

4e1s


Resolution: 2.263→29.787 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.193 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 709 5.1 %RANDOM
Rwork0.188 ---
all0.1915 15222 --
obs0.1915 14016 90.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 96.44 Å2 / Biso mean: 50.288 Å2 / Biso min: 16.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.15 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.263→29.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 283 117 2360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212279
X-RAY DIFFRACTIONr_angle_refined_deg1.9542.0323003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.56523.945109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78715314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5531515
X-RAY DIFFRACTIONr_chiral_restr0.130.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211679
X-RAY DIFFRACTIONr_mcbond_it0.7821.51209
X-RAY DIFFRACTIONr_mcangle_it1.44421922
X-RAY DIFFRACTIONr_scbond_it2.56631070
X-RAY DIFFRACTIONr_scangle_it3.9134.51081
LS refinement shellResolution: 2.263→2.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 30 -
Rwork0.27 626 -
all-656 -
obs--57.9 %
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)
15.39043.39223.48249.38146.45757.36550.1125-0.1072-0.1053-0.54730.05280.0423-0.2469-0.3476-0.16520.07450.0203-0.00640.20560.07930.0685-22.586530.15437.0525
28.44277.94122.206311.89862.76232.4995-0.0411-0.0830.1186-0.1995-0.00390.0982-0.085-0.13050.04510.02860.0279-0.00550.126-0.04020.0006-12.24533.068813.433
31.2928-0.82040.33973.1343-0.86922.42550.03510.0728-0.0607-0.27580.0049-0.00850.32470.0131-0.04010.0639-0.0198-0.01510.0738-0.02110.0363-8.227224.93944.8581
40.14195.8049-1.60239.6983-4.536619.62120.3165-0.6737-0.3176-0.43-0.60960.21990.62960.43560.29310.4-0.0726-0.19090.11080.01050.0984-9.44519.1942-2.2111
51.6439-0.50070.05771.4118-0.19311.22680.05570.0236-0.0984-0.1277-0.07730.46170.0444-0.19490.02160.1436-0.005-0.05960.1669-0.00330.1349-18.957131.34231.9355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A146 - 163
2X-RAY DIFFRACTION2A164 - 192
3X-RAY DIFFRACTION3A193 - 295
4X-RAY DIFFRACTION4A298 - 311
5X-RAY DIFFRACTION5A312 - 390

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