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- PDB-3ml3: Crystal structure of the IcsA autochaperone region -

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Basic information

Entry
Database: PDB / ID: 3ml3
TitleCrystal structure of the IcsA autochaperone region
ComponentsOuter membrane protein icsA autotransporter
KeywordsPROTEIN TRANSPORT / BETA HELIX / BETA SANDWICH
Function / homology
Function and homology information


symbiont-mediated cell-to-cell migration in host / cell tip / cell outer membrane / periplasmic space / cell adhesion / cell surface / extracellular region
Similarity search - Function
: / VirG insertion domain (VID) / Autotransporter-associated beta strand repeat / Autochaperone domain type 1 / Passenger-associated-transport-repeat / Autochaperone Domain Type 1 / : / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain ...: / VirG insertion domain (VID) / Autotransporter-associated beta strand repeat / Autochaperone domain type 1 / Passenger-associated-transport-repeat / Autochaperone Domain Type 1 / : / Autotransporter beta-domain / Outer membrane autotransporter barrel / 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
Outer membrane autotransporter IcsA
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDiezmann, D. / Kuhnel, K.
CitationJournal: J.Bacteriol. / Year: 2011
Title: Crystal Structure of the Autochaperone Region from the Shigella flexneri Autotransporter IcsA
Authors: Kuhnel, K. / Diezmann, D.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein icsA autotransporter


Theoretical massNumber of molelcules
Total (without water)20,2421
Polymers20,2421
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.220, 104.220, 61.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Outer membrane protein icsA autotransporter / Outer membrane protein icsA / Outer membrane protein icsA translocator


Mass: 20242.346 Da / Num. of mol.: 1 / Fragment: IcsA autochaperone region, UNP residues 591-758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: CP0182, icsA, virG / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7BCK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsV725A IS A NATURAL VARIANT ACCORDING TO DATABASE UNIPROTKB/SWISS-PROT Q7BCK4 (ICSA_SHIFL).

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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: 4.77 Å3/Da / Density % sol: 74.21 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6
Details: 17% PEG 4000, 10% isopropanol, 0.1M sodium citrate, pH 6.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 25896 / Num. obs: 24863 / % possible obs: 96 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Biso Wilson estimate: 45.7 Å2 / Rsym value: 0.046 / Net I/σ(I): 25.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3167 / Rsym value: 0.606 / % possible all: 90.3

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Processing

Software
NameVersionClassification
SHELXSphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→23.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.565 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1294 5 %RANDOM
Rwork0.19644 ---
obs0.19754 24557 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.925 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.11 Å20 Å2
2---0.21 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2→23.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 0 80 1225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211176
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9361598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.926.2548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.548153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02882
X-RAY DIFFRACTIONr_nbd_refined0.1790.2423
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.23
X-RAY DIFFRACTIONr_mcbond_it1.1011.5789
X-RAY DIFFRACTIONr_mcangle_it1.87221234
X-RAY DIFFRACTIONr_scbond_it2.4653435
X-RAY DIFFRACTIONr_scangle_it4.364.5361
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 96
Rwork0.269 1804

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