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- PDB-3emo: Crystal structure of transmembrane Hia 973-1098 -

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Basic information

Entry
Database: PDB / ID: 3emo
TitleCrystal structure of transmembrane Hia 973-1098
ComponentsHia (Adhesin)
KeywordsMEMBRANE PROTEIN/CELL ADHESION / transmembrane / outer membrane / Hia adhesin / trimeric autotransporter / MEMBRANE PROTEIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


outer membrane / cell surface
Similarity search - Function
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 / GSPII I/J protein-like / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter 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 / GSPII I/J protein-like / 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 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Hia (Adhesin)
A: Hia (Adhesin)
B: Hia (Adhesin)


Theoretical massNumber of molelcules
Total (without water)48,9573
Polymers48,9573
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-88 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.300, 45.811, 56.423
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hia (Adhesin)


Mass: 16319.004 Da / Num. of mol.: 3 / Fragment: UNP residues 937-1098
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pASK-iba12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48152

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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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 10069 / Num. obs: 8519 / % possible obs: 84.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.151 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.15 / % possible all: 60.8

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Processing

Software
NameClassification
DNAdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2gr7

2gr7


Resolution: 3→29.57 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.699 / 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
Rfree0.289 1017 10.08 %random
Rwork0.221 9072 --
obs-8519 97.24 %-
Solvent computationBsol: 41.496 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 116.4 Å2 / Biso mean: 61.602 Å2 / Biso min: 34.94 Å2
Baniso -1Baniso -2Baniso -3
1-25.373 Å2-0 Å2-39.637 Å2
2---14.451 Å2-0 Å2
3----10.921 Å2
Refinement stepCycle: LAST / Resolution: 3→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 0 0 2605
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.9841
X-RAY DIFFRACTIONf_bond_d0.0061
X-RAY DIFFRACTIONf_chiral_restr0.0641
X-RAY DIFFRACTIONf_dihedral_angle_d18.481
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.1081
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
3-3.0580.273494X-RAY DIFFRACTION1887
3.058-3.120.295454X-RAY DIFFRACTION1883
3.12-3.1880.267489X-RAY DIFFRACTION1885
3.188-3.2620.257499X-RAY DIFFRACTION1886
3.262-3.3440.235501X-RAY DIFFRACTION1890
3.344-3.4340.232473X-RAY DIFFRACTION1884
3.434-3.5350.224506X-RAY DIFFRACTION1887
3.535-3.6490.215487X-RAY DIFFRACTION1887
3.649-3.7790.206523X-RAY DIFFRACTION1888
3.779-3.930.178497X-RAY DIFFRACTION1890
3.93-4.1090.188508X-RAY DIFFRACTION1887
4.109-4.3250.173517X-RAY DIFFRACTION1889
4.325-4.5960.184510X-RAY DIFFRACTION1888
4.596-4.950.198510X-RAY DIFFRACTION1889
4.95-5.4470.212511X-RAY DIFFRACTION1890
5.447-6.2320.238529X-RAY DIFFRACTION1889
6.232-7.840.226525X-RAY DIFFRACTION1888
7.84-37.5480.25539X-RAY DIFFRACTION1887

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