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- PDB-4ql0: Crystal Structure Analysis of the Membrane Transporter FhaC (doub... -

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Basic information

Entry
Database: PDB / ID: 4ql0
TitleCrystal Structure Analysis of the Membrane Transporter FhaC (double mutant V169T, I176N)
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Filamentous hemagglutinin transporter protein FhaC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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: 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.
#2: Journal: Mol.Microbiol. / Year: 2011
Title: Substrate recognition by the POTRA domains of TpsB transporter FhaC
Authors: Delattre, A.S. / Saint, N. / Clantin, B. / Willery, E. / Lippens, G. / Locht, C. / Villeret, V. / Jacob-Dubuisson, F.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Derived calculations
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Filamentous hemagglutinin transporter protein FhaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,35910
Polymers61,4161
Non-polymers1,9439
Water1,35175
1
A: Filamentous hemagglutinin transporter protein FhaC
hetero molecules

A: Filamentous hemagglutinin transporter protein FhaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,71820
Polymers122,8322
Non-polymers3,88618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11900 Å2
ΔGint-20 kcal/mol
Surface area55410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.380, 136.950, 110.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

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


Mass: 61415.758 Da / Num. of mol.: 1 / Mutation: V169T, I176N
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: pFJD138 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-OMP5 / References: UniProt: P35077
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 81 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 34% PEG 1000, 1% beta-octyl-glucoside, 500mM imidazole, 26mg/ml protein, 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: 0.93928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2010
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 2.5→41.95 Å / Num. all: 28332 / Num. obs: 28332 / % possible obs: 99.69 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 74.17 Å2
Reflection shellResolution: 2.5→2.65 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4QKY

4qky


Resolution: 2.5→41.95 Å / Cor.coef. Fo:Fc: 0.9141 / Cor.coef. Fo:Fc free: 0.8894 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.326 / SU Rfree Blow DPI: 0.246 / Stereochemistry target values: Engh & Huber / Details: isomorphous replacement using pdb entry 4QKY
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 2739 9.67 %RANDOM
Rwork0.217 ---
all0.221 28332 --
obs0.221 28332 99.69 %-
Displacement parametersBiso mean: 78.93 Å2
Baniso -1Baniso -2Baniso -3
1--5.9492 Å20 Å20 Å2
2--4.3791 Å20 Å2
3---1.5701 Å2
Refine analyzeLuzzati coordinate error obs: 0.503 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 130 75 4292
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2363SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1214HARMONIC5
X-RAY DIFFRACTIONt_it8506HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion531SEMIHARMONIC5
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_contact8882SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8506HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15286HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion3.3
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3419 259 8.74 %
Rwork0.2425 2705 -
all0.2508 2964 -
obs-2964 99.69 %
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)
10.392-1.44340.12574.04962.89441.12190.0194-0.01580.1682-0.0119-0.1019-0.0796-0.072-0.12410.08250.1570.1520.068-0.12860.0507-0.1952-27.211630.618661.2646
21.75850.8977-1.95980.73090.24727.915-0.0527-0.3146-0.0679-0.00110.0128-0.07190.31850.54420.03990.04890.00860.0296-0.09330.005-0.118215.76873.087831.1391
32.13890.7102-0.25382.899-0.56910.9944-0.01690.13830.1066-0.06270.02690.2392-0.0167-0.0093-0.01010.1006-0.05010.0274-0.0799-0.0236-0.09287.773711.73210.9906
41.11560.9782-0.32613.2609-1.64142.61440.2824-0.09920.25860.1664-0.2518-0.0805-0.41660.3802-0.0306-0.0953-0.1520.152-0.14690.023-0.297731.780235.7418-9.6124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|44 }A4 - 44
2X-RAY DIFFRACTION2{ A|45 - A|133 }A45 - 133
3X-RAY DIFFRACTION3{ A|134 - A|208 }A134 - 208
4X-RAY DIFFRACTION4{ A|209 - A|554 }A209 - 554

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