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- PDB-3ncx: Crystal structure of EHEC O157:H7 intimin mutant -

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Basic information

Entry
Database: PDB / ID: 3ncx
TitleCrystal structure of EHEC O157:H7 intimin mutant
ComponentsIntimin adherence protein
KeywordsCELL ADHESION / intimin tir
Function / homology
Function and homology information


cell outer membrane / cell adhesion
Similarity search - Function
Intimin, C-terminal / Intimin C-type lectin domain / Immunoglobulin-like - #1080 / 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 ...Intimin, C-terminal / Intimin C-type lectin domain / Immunoglobulin-like - #1080 / 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 / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYi, Y. / Gao, F. / Gao, G.F. / Zou, Q.M.
CitationJournal: Plos One / Year: 2010
Title: Crystal Structure of EHEC Intimin: Insights into the Complementarity between EPEC and EHEC
Authors: Yi, Y. / Ma, Y. / Gao, F. / Mao, X. / Peng, H. / Feng, Y. / Fan, Z. / Wang, G. / Guo, G. / Yan, J. / Zeng, H. / Zou, Q.M. / Gao, G.F.
History
DepositionJun 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
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: Intimin adherence protein
B: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)41,4442
Polymers41,4442
Non-polymers00
Water4,738263
1
A: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)20,7221
Polymers20,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)20,7221
Polymers20,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.771, 92.488, 100.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Intimin adherence protein / Intimin


Mass: 20722.170 Da / Num. of mol.: 2 / Fragment: residues 747-934 / Mutation: Y916N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: EHEC / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / References: UniProt: C6UYL6, UniProt: P43261*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→41.98 Å / Num. all: 13058 / Num. obs: 13058 / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.132

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
PHENIX(phenix.refine: 1.6.2_432)refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NCW

3ncw


Resolution: 2.6→41.977 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8519 / SU ML: 0.35 / σ(F): 0 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 641 4.93 %
Rwork0.213 12365 -
obs0.2157 13006 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.594 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 98.21 Å2 / Biso mean: 30.6372 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.4916 Å2-0 Å2-0 Å2
2---1.7775 Å2-0 Å2
3----1.7141 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 0 263 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032925
X-RAY DIFFRACTIONf_angle_d0.6183979
X-RAY DIFFRACTIONf_dihedral_angle_d12.7651041
X-RAY DIFFRACTIONf_chiral_restr0.043452
X-RAY DIFFRACTIONf_plane_restr0.005502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80070.31781160.26812436X-RAY DIFFRACTION100
2.8007-3.08250.34481410.25162411X-RAY DIFFRACTION100
3.0825-3.52830.30951220.21412471X-RAY DIFFRACTION100
3.5283-4.44450.22431310.18482473X-RAY DIFFRACTION100
4.4445-41.98230.22271310.19682574X-RAY DIFFRACTION98

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