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- PDB-3njt: Crystal structure of the R450A mutant of the membrane protein FhaC -

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Basic information

Entry
Database: PDB / ID: 3njt
TitleCrystal structure of the R450A mutant of the membrane protein FhaC
ComponentsFilamentous hemagglutinin transporter protein fhaC
KeywordsPROTEIN TRANSPORT / Membrane protein / beta barrel / Omp85/TpsB transporter family
Function / homology
Function and homology information


type V protein secretion system complex / protein secretion by the type V secretion system / porin activity / pore complex / protein transmembrane transporter activity / monoatomic ion transport / cell outer membrane
Similarity search - Function
Two partner secretion pathway transporter / ShlB, POTRA domain / : / POTRA domain / Haemolysin activator HlyB, C-terminal / Haemolysin secretion/activation protein ShlB/FhaC/HecB / Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac ...Two partner secretion pathway transporter / ShlB, POTRA domain / : / POTRA domain / Haemolysin activator HlyB, C-terminal / Haemolysin secretion/activation protein ShlB/FhaC/HecB / Polypeptide-transport-associated, ShlB-type / POTRA domain, ShlB-type / membrane protein fhac: a member of the omp85/tpsb transporter family / membrane protein fhac / POTRA domain / POTRA domain profile. / Porin / Ubiquitin-like (UB roll) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Filamentous hemagglutinin transporter protein FhaC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsClantin, B. / Delattre, A.S. / Jacob-Dubuisson, F. / Villeret, V.
CitationJournal: Febs J. / Year: 2010
Title: Functional importance of a conserved sequence motif in FhaC, a prototypic member of the TpsB/Omp85 superfamily.
Authors: Delattre, A.S. / Clantin, B. / Saint, N. / Locht, C. / Villeret, V. / Jacob-Dubuisson, F.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamentous hemagglutinin transporter protein fhaC


Theoretical massNumber of molelcules
Total (without water)62,5981
Polymers62,5981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.550, 139.390, 113.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Filamentous hemagglutinin transporter protein fhaC / TpsB transporter


Mass: 62598.031 Da / Num. of mol.: 1 / Fragment: UNP residues 34-584 / Mutation: R450A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama 1 / Gene: fhaC, BP1884 / Plasmid: pFJD118-R450A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 OMP5 / References: UniProt: P35077

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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: 3.39 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 1000, 1% B-octyl-glucoside, 500 mM imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.5→48.6 Å / Num. obs: 11007 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 30
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GDZ

2gdz


Resolution: 3.5→48.56 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 5589898 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.38 1113 10.1 %RANDOM
Rwork0.35 ---
obs0.35 11007 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 106.488 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 105.5 Å2
Baniso -1Baniso -2Baniso -3
1-39.04 Å20 Å20 Å2
2---21.59 Å20 Å2
3----17.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å1.06 Å
Refinement stepCycle: LAST / Resolution: 3.5→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 0 0 3514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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