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- PDB-6gus: CRYSTAL STRUCTURE OF PROTEIN E FROM NON-TYPEABLE HAEMOPHILUS INFL... -

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Basic information

Entry
Database: PDB / ID: 6gus
TitleCRYSTAL STRUCTURE OF PROTEIN E FROM NON-TYPEABLE HAEMOPHILUS INFLUENZAE
ComponentsSurface-adhesin protein
KeywordsCELL ADHESION / BACTERIAL PROTEIN / SURFACE ADHESIN / PROT-E / SURFACE LIPOPROTEIN. / ADHESIN
Function / homology
Function and homology information


cell outer membrane / cell surface
Similarity search - Function
Surface-adhesin protein E, Pasteurellaceae / Surface-adhesin protein E-like / Surface-adhesin protein E / Surface-adhesin protein E / Surface-adhesin protein E / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Surface-adhesin protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.92 Å
AuthorsSomers, D.
CitationJournal: Infect.Immun. / Year: 2019
Title: Design and Characterization of Protein E-PilA, a Candidate Fusion Antigen for Nontypeable Haemophilus influenzae Vaccine.
Authors: Blais, N. / Somers, D. / Faubert, D. / Labbe, S. / Castado, C. / Ysebaert, C. / Gagnon, L.P. / Champagne, J. / Gagne, M. / Martin, D.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Surface-adhesin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3255
Polymers18,0091
Non-polymers3164
Water1,802100
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-17 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.670, 77.670, 66.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-377-

HOH

21A-383-

HOH

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Components

#1: Protein Surface-adhesin protein / protein E


Mass: 18009.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: pe / Production host: Escherichia coli (E. coli) / References: UniProt: S5ZIQ9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG3350, AMMONIUM SULPHATE, SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.92→30.751 Å / Num. obs: 14861 / % possible obs: 98.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 39.02 Å2 / Rpim(I) all: 0.013 / Rrim(I) all: 0.034 / Rsym value: 0.029 / Net I/av σ(I): 13.5 / Net I/σ(I): 28.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.92-1.977.20.4661.710840.2010.5450.46697.6
1.97-2.027.20.3232.410780.140.3780.32399.2
2.02-2.087.10.2463.210470.1090.2940.24698.9
2.08-2.157.10.1834.29960.080.2160.18398.8
2.15-2.2270.1495.29990.0660.1770.14999.4
2.22-2.36.80.1196.49490.0530.140.11999.4
2.3-2.386.70.1047.39200.0480.1240.10499.1
2.38-2.486.20.0878.78720.0420.1050.08797.8
2.48-2.596.70.0612.17780.0280.0740.0693.9
2.59-2.727.20.04914.48200.0220.0590.04999.8
2.72-2.867.20.0417.77780.0180.0480.0499.6
2.86-3.047.10.03320.47370.0140.0390.03399.2
3.04-3.257.10.02724.16830.0120.0320.027100
3.25-3.516.90.02423.96540.0110.0290.024100
3.51-3.846.70.02327.75950.010.0270.023100
3.84-4.296.40.02127.35420.0090.0240.02199.8
4.29-4.966.20.01831.44370.0090.0220.01891.9
4.96-6.077.30.02284030.0080.0230.0299.7
6.07-8.597.30.02126.93150.0090.0250.021100
8.59-30.7516.90.02224.91740.010.0270.02295.9

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Processing

Software
NameVersionClassification
XDSDecember 31, 2011data reduction
XSCALEDecember 31, 2011data scaling
SCALA3.3.20data scaling
SHARP2.9.2BETAphasing
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MIR / Resolution: 1.92→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.085 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.146
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 754 5.1 %RANDOM
Rwork0.1847 ---
obs0.1872 14093 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.24 Å2 / Biso mean: 58.16 Å2 / Biso min: 30.35 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20 Å2
2---2.52 Å20 Å2
3---5.03 Å2
Refinement stepCycle: final / Resolution: 1.92→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 18 100 1300
Biso mean--73.18 61.67 -
Num. residues----147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191234
X-RAY DIFFRACTIONr_bond_other_d0.0010.021132
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9471682
X-RAY DIFFRACTIONr_angle_other_deg0.74832592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88224.28663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84215190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.006157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02299
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 62 -
Rwork0.314 1012 -
all-1074 -
obs--97.64 %

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