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- PDB-3emi: Crystal structure of Hia 307-422 non-adhesive domain -

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Basic information

Entry
Database: PDB / ID: 3emi
TitleCrystal structure of Hia 307-422 non-adhesive domain
ComponentsHia (Adhesin)
KeywordsCELL ADHESION / non-adhesive domain / Hia adhesin / trimeric autotransporter / Haemophilus influenzae
Function / homology
Function and homology information


outer membrane / cell surface
Similarity search - Function
Trimeric adhesin / Trimeric adhesin / Trimeric autotransporter adhesin, tryptophan-ring motif / Trimeric autotransporter adhesin, putative GIN domain / Trimeric adhesin / Trimeric autotransporter adhesin, Trp ring domain / Tryptophan-ring motif of head of Trimeric autotransporter adhesin / HiaBD2_N domain of Trimeric autotransporter adhesin (GIN) / Trimeric autotransporter adhesin Trp ring domain / Trimeric autotransporter adhesin YadA-like, stalk domain ...Trimeric adhesin / Trimeric adhesin / Trimeric autotransporter adhesin, tryptophan-ring motif / Trimeric autotransporter adhesin, putative GIN domain / Trimeric adhesin / Trimeric autotransporter adhesin, Trp ring domain / Tryptophan-ring motif of head of Trimeric autotransporter adhesin / HiaBD2_N domain of Trimeric autotransporter adhesin (GIN) / Trimeric autotransporter adhesin Trp ring domain / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMeng, G. / Waksman, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Repetitive Architecture of the Haemophilus influenzae Hia Trimeric Autotransporter
Authors: Meng, G. / St Geme, J.W. / Waksman, G.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hia (Adhesin)


Theoretical massNumber of molelcules
Total (without water)12,0471
Polymers12,0471
Non-polymers00
Water4,396244
1
A: Hia (Adhesin)

A: Hia (Adhesin)

A: Hia (Adhesin)


Theoretical massNumber of molelcules
Total (without water)36,1423
Polymers36,1423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8260 Å2
ΔGint-68 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.864, 53.864, 151.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-46-

HOH

21A-88-

HOH

31A-94-

HOH

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Components

#1: Protein Hia (Adhesin)


Mass: 12047.246 Da / Num. of mol.: 1 / Fragment: UNP residues 307-422 / Mutation: I324M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(B834) / References: UniProt: Q48152
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9785, 0.9790, 0.9750
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.9791
30.9751
ReflectionResolution: 1.8→30 Å / Num. obs: 12852 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.6 % / Biso Wilson estimate: 15.127 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 42
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 26 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 11.3 / Rsym value: 0.27 / % possible all: 99.9

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Processing

Software
NameClassification
DNAdata collection
SHELXSphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.43 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.878 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.198 643 5.03 %random
Rwork0.162 12139 --
obs-12782 99.46 %-
Solvent computationBsol: 54.433 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 63.5 Å2 / Biso mean: 21.274 Å2 / Biso min: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.963 Å20 Å20 Å2
2---0.963 Å20 Å2
3---1.926 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 0 244 1030
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.8811
X-RAY DIFFRACTIONf_bond_d0.0051
X-RAY DIFFRACTIONf_chiral_restr0.0571
X-RAY DIFFRACTIONf_dihedral_angle_d10.9261
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.1161
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.8-1.8260.146473X-RAY DIFFRACTION2493
1.826-1.8530.152490X-RAY DIFFRACTION2494
1.853-1.8820.134470X-RAY DIFFRACTION2493
1.882-1.9130.132508X-RAY DIFFRACTION2496
1.913-1.9460.136483X-RAY DIFFRACTION2493
1.946-1.9810.137487X-RAY DIFFRACTION2494
1.981-2.0190.141474X-RAY DIFFRACTION2493
2.019-2.060.139499X-RAY DIFFRACTION2495
2.06-2.1050.127483X-RAY DIFFRACTION2495
2.105-2.1540.134499X-RAY DIFFRACTION2493
2.154-2.2080.141482X-RAY DIFFRACTION2494
2.208-2.2680.131513X-RAY DIFFRACTION2496
2.268-2.3350.136505X-RAY DIFFRACTION2494
2.335-2.410.15482X-RAY DIFFRACTION2494
2.41-2.4960.159508X-RAY DIFFRACTION2496
2.496-2.5960.191509X-RAY DIFFRACTION2495
2.596-2.7140.176512X-RAY DIFFRACTION2496
2.714-2.8570.165512X-RAY DIFFRACTION2494
2.857-3.0360.18515X-RAY DIFFRACTION2496
3.036-3.270.16499X-RAY DIFFRACTION2493
3.27-3.5990.164534X-RAY DIFFRACTION2494
3.599-4.120.166531X-RAY DIFFRACTION2495
4.12-5.1890.161550X-RAY DIFFRACTION2495
5.189-39.7430.227621X-RAY DIFFRACTION2496

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