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- PDB-4qky: Crystal Structure Analysis of the Membrane Transporter FhaC -

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Basic information

Entry
Database: PDB / ID: 4qky
TitleCrystal Structure Analysis of the Membrane Transporter FhaC
ComponentsFilamentous hemagglutinin transporter protein FhaC
KeywordsPROTEIN TRANSPORT / BETA BARREL / POTRA DOMAIN / outer membrane
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane / protein transport
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 / POTRA domain ...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
PHOSPHATE ION / Filamentous hemagglutinin transporter protein FhaC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsMaier, T. / Clantin, B. / Gruss, F. / Dewitte, F. / Delattre, A.S. / Jacob-Dubuisson, F. / Hiller, S. / Villeret, V.
Citation
Journal: Nat Commun / Year: 2015
Title: Conserved Omp85 lid-lock structure and substrate recognition in FhaC
Authors: Maier, T. / Clantin, B. / Gruss, F. / Dewitte, F. / Delattre, A.S. / Jacob-Dubuisson, F. / Hiller, S. / Villeret, V.
#1: Journal: To be Published
Title: Translocation path of a substrate protein through its Omp85 transporter
Authors: Baud, C. / Guerin, J. / Petit, E. / Lesne, E. / Dupre, E. / Locht, C. / Jacob-Dubuisson, F.
#2: Journal: Science / Year: 2007
Title: Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily
Authors: Clantin, B. / Delattre, A.S. / Rucktooa, P. / Saint, N. / Meli, A.C. / Locht, C. / Jacob-Dubuisson, F. / Villeret, V.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 22, 2014ID: 2QDZ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Filamentous hemagglutinin transporter protein FhaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5082
Polymers61,4131
Non-polymers951
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.600, 136.650, 112.270
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: 61412.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: BP1884, fhaC / Plasmid: PT7FCW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-OMP5 / References: UniProt: P35077
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 63.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 32% PEG 1000, 1% beta-octyl-glucoside, 400mM imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2005
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978951 Å / Relative weight: 1
ReflectionResolution: 2.9→39.34 Å / Num. all: 18626 / Num. obs: 18626 / % possible obs: 98.77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 87.88 Å2
Reflection shellResolution: 2.9→2.95 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→39.34 Å / Cor.coef. Fo:Fc: 0.8664 / Cor.coef. Fo:Fc free: 0.8356 / SU R Cruickshank DPI: 0.648 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.606 / SU Rfree Blow DPI: 0.353 / SU Rfree Cruickshank DPI: 0.364 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 1854 9.95 %RANDOM
Rwork0.2218 ---
all0.2274 18626 --
obs0.2274 18626 98.77 %-
Displacement parametersBiso mean: 91.46 Å2
Baniso -1Baniso -2Baniso -3
1--22.9631 Å20 Å20 Å2
2--11.3135 Å20 Å2
3---11.6496 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: LAST / Resolution: 2.9→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 5 0 3731
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes559HARMONIC5
X-RAY DIFFRACTIONt_it3805HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4008SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3805HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5151HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion3.6
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.263 279 9.44 %
Rwork0.2144 2675 -
all0.2189 2954 -
obs-2954 98.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10-1.0502-0.00655.4566-1.25672.907-0.0544-0.12940.129-0.0670.0325-0.0468-0.143-0.03480.02190.06250.152-0.0226-0.00270.0385-0.2201-30.275533.323864.1735
22.8927-0.8358-0.62332.1915-0.61248.3155-0.0824-0.54420.23870.3616-0.0052-0.32040.04250.31760.08760.1026-0.02360.0426-0.107-0.0395-0.197417.01342.444228.7658
33.20250.46420.54623.0431-1.66146.3390.10440.38150.22490.39260.11630.5442-0.5442-0.4532-0.2208-0.09080.04610.1168-0.2042-0.0628-0.03258.721811.86981.0701
41.85571.0307-0.2632.8613-0.84832.38190.27490.13940.28490.1236-0.13050.0649-0.54420.1629-0.1444-0.0971-0.1520.1328-0.1680.0489-0.236431.223435.5978-8.8335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|7 - A|35 }A7 - 35
2X-RAY DIFFRACTION2{ A|58 - A|133 }A58 - 133
3X-RAY DIFFRACTION3{ A|134 - A|208 }A134 - 208
4X-RAY DIFFRACTION4{ A|209 - A|554 }A209 - 554

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