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- PDB-3ncw: Crystal structure of EHEC O157:H7 intimin -

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Basic information

Entry
Database: PDB / ID: 3ncw
TitleCrystal structure of EHEC O157:H7 intimin
ComponentsIntimin adherence protein
KeywordsCELL ADHESION / CELL MEMBRANE / IMMUNOGLOBULIN-LIKE FOLD / C-TYPE and LECTIN-LIKE FOLD
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 / : / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) ...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 / : / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / 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: 2.8 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Intimin adherence protein
D: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)82,6924
Polymers82,6924
Non-polymers00
Water2,792155
1
A: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)20,6731
Polymers20,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)20,6731
Polymers20,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)20,6731
Polymers20,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Intimin adherence protein


Theoretical massNumber of molelcules
Total (without water)20,6731
Polymers20,6731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)235.157, 44.810, 129.116
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Intimin adherence protein / Intimin


Mass: 20673.098 Da / Num. of mol.: 4 / Fragment: residues 747-934
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


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: 2.8→46.21 Å / Num. obs: 32396 / % possible obs: 96.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 4.1 / Num. measured all: 109738
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.4 / % possible all: 92.7

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F00

1f00


Resolution: 2.8→20 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 3229 9.6 %RANDOM
Rwork0.2537 29069 --
all-33523 --
obs-32298 96.3 %-
Solvent computationBsol: 24.5136 Å2
Displacement parametersBiso max: 100.68 Å2 / Biso mean: 29.5956 Å2 / Biso min: 1.07 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å2-0.29 Å2
2---5.68 Å20 Å2
3---3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 0 155 5795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.646
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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