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- PDB-6gut: CRYSTAL STRUCTURE OF NON-TYPEABLE HAEMOPHILUS INFLUENZAE PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 6gut
TitleCRYSTAL STRUCTURE OF NON-TYPEABLE HAEMOPHILUS INFLUENZAE PROTEIN E AND PILA EXPRESSED AS A SINGLE-CHAIN CHIMERIC PROTEIN
Components23S rRNA pseudouridine synthase D,PilA
KeywordsCELL ADHESION / BACTERIAL PROTEIN / SURFACE ADHESIN / PROT-E / PILA / SURFACE LIPOPROTEIN. / ADHESIN / PILIN / TYPE IV PILUS
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Surface-adhesin protein E-like / Surface-adhesin protein E / Surface-adhesin protein E / Surface-adhesin protein E / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 23S rRNA pseudouridine synthase D / PilA
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 1.2May 1, 2024Group: 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
A: 23S rRNA pseudouridine synthase D,PilA
B: 23S rRNA pseudouridine synthase D,PilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,25611
Polymers57,5062
Non-polymers7509
Water11,313628
1
A: 23S rRNA pseudouridine synthase D,PilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0004
Polymers28,7531
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 23S rRNA pseudouridine synthase D,PilA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2567
Polymers28,7531
Non-polymers5026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.618, 83.458, 59.049
Angle α, β, γ (deg.)90.000, 102.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-667-

HOH

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Components

#1: Protein 23S rRNA pseudouridine synthase D,PilA


Mass: 28753.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: rluD, CGSHi22121_05660, pilA / Production host: Escherichia coli (E. coli) / References: UniProt: A4MX90, UniProt: Q5D8E3
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG4000, AMMONIUM SULPHATE, SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.63→47.244 Å / Num. obs: 75506 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.57 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Rsym value: 0.062 / Net I/av σ(I): 6.3 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.63-1.693.30.5431.473860.3510.6490.54399.4
1.69-1.753.50.3981.971240.2490.470.39899.7
1.75-1.823.50.2742.868670.1730.3250.27499.7
1.82-1.93.40.189466510.120.2250.18999.6
1.9-23.20.1345.562210.0880.1610.13499.4
2-2.13.50.1076.960490.0660.1260.10799.8
2.1-2.233.50.0878.356710.0540.1030.08799.7
2.23-2.393.40.0759.353680.0470.0890.07599.6
2.39-2.583.20.06610.349400.0430.0790.06699.4
2.58-2.823.50.0611.145980.0380.0710.0699.7
2.82-3.163.40.05611.741230.0350.0660.05699.6
3.16-3.643.10.05112.236540.0330.0610.05198.4
3.64-4.463.40.04912.630940.030.0570.04999.6
4.46-6.313.40.04712.124110.0290.0560.04799.6
6.31-47.2443.30.04611.713490.0290.0550.04698.8

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Processing

Software
NameVersionClassification
XDSMarch 15th 2012data reduction
XSCALEMarch 15th 2012data scaling
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE

Resolution: 1.63→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.728 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3797 5 %RANDOM
Rwork0.1774 ---
obs0.179 71708 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.24 Å2 / Biso mean: 24.587 Å2 / Biso min: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å2-0.02 Å2
2---0.56 Å20 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 43 628 4314
Biso mean--50.96 40.04 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023777
X-RAY DIFFRACTIONr_bond_other_d0.0010.022438
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9555152
X-RAY DIFFRACTIONr_angle_other_deg0.8463.0045973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4385477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57825.031161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.62715604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0421514
X-RAY DIFFRACTIONr_chiral_restr0.080.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
LS refinement shellResolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 276 -
Rwork0.318 5117 -
all-5393 -
obs--99.12 %

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