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- PDB-6nqw: Flagellar protein FcpA from Leptospira biflexa - hexagonal form -

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Basic information

Entry
Database: PDB / ID: 6nqw
TitleFlagellar protein FcpA from Leptospira biflexa - hexagonal form
ComponentsFlagellar coiling protein A
KeywordsPROTEIN FIBRIL / flagellar filament
Function / homologyPHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesLeptospira biflexa serovar Patoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsSan Martin, F. / Trajtenberg, F. / Larrieux, N. / Buschiazzo, A.
Citation
Journal: Elife / Year: 2020
Title: An asymmetric sheath controls flagellar supercoiling and motility in the Leptospira spirochete
Authors: Gibson, K. / Trajtenberg, F. / Brady, M. / San Martin, F. / Mechaly, A. / Wunder, E. / Picardeau, M. / Ko, A. / Buschiazzo, A. / Sindelar, C.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.
Authors: Fabiana San Martin / Ariel E Mechaly / Nicole Larrieux / Elsio A Wunder / Albert I Ko / Mathieu Picardeau / Felipe Trajtenberg / Alejandro Buschiazzo /
Abstract: The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and ...The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.
History
DepositionJan 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Flagellar coiling protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,83015
Polymers32,3861
Non-polymers1,44414
Water4,288238
1
A: Flagellar coiling protein A
hetero molecules

A: Flagellar coiling protein A
hetero molecules

A: Flagellar coiling protein A
hetero molecules

A: Flagellar coiling protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,31960
Polymers129,5434
Non-polymers5,77756
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area19950 Å2
ΔGint-71 kcal/mol
Surface area51240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.360, 132.360, 67.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

#1: Protein Flagellar coiling protein A


Mass: 32385.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris) (bacteria)
Strain: Patoc 1 / ATCC 23582 / Paris / Gene: LEPBI_I0267 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2 (DE3) / References: UniProt: B0STJ8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: PEG 8000, Na/K phosphate, NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→67.36 Å / Num. obs: 27914 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.67 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.066 / Rrim(I) all: 0.166 / Net I/σ(I): 23.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.946.82.12817420.2180.882.30999.3
9.1-67.364.40.0473200.9770.0250.05398.5

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→58.08 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1494 5.36 %RANDOM
Rwork0.194 ---
obs0.195 27881 99.4 %-
Displacement parametersBiso max: 141.18 Å2 / Biso mean: 40.76 Å2 / Biso min: 14.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.1875 Å20 Å20 Å2
2---1.1875 Å20 Å2
3---2.375 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.9→58.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 90 240 2309
Biso mean--61.17 50.51 -
Num. residues----237
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d796SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes363HARMONIC5
X-RAY DIFFRACTIONt_it2161HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion259SEMIHARMONIC5
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_contact2690SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2161HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2907HARMONIC20.86
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion17.71
LS refinement shellResolution: 1.9→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.268 35 6.27 %
Rwork0.2795 523 -
all0.2788 558 -
obs--99.09 %
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)
12.56191.5220.21370.9035-1.41064.6867-0.0525-0.52120.11010.30150.01470.1238-0.7999-0.22010.03770.05120.04330.01230.0298-0.0477-0.151242.478222.894928.0681
22.2368-1.0811.55311.7895-0.41582.6176-0.0905-0.44290.19520.253-0.11520.0904-0.1482-0.18250.2057-0.0687-0.00090.0301-0.0347-0.01130.037229.75637.305330.8527
38.3866-3.04762.76642.2047-1.08761.0836-0.01810.0321-0.35910.1294-0.07680.0207-0.00710.20520.0949-0.09260.0063-0.0027-0.02780.05390.024442.2375-2.565925.493
41.50510.0161-3.3771-0.4831-0.2672.4750.0444-0.0365-0.2281-0.04780.0569-0.21110.2411-0.1309-0.1013-0.02980.0203-0.02220.12420.02210.206972.7116-12.29925.7458
58.1628-1.83920.89140.77590.227500.06510.6246-0.42390.0038-0.04640.0280.03720.1685-0.0187-0.04490.0587-0.00860.0463-0.01230.081249.9521-3.462116.7384
65.5993-0.9707-0.10591.2314-0.11260.10370.09760.07810.1602-0.0445-0.14080.111-0.05140.04090.0432-0.07620.0397-0.0186-0.0661-0.01620.015931.680410.749817.7174
74.62661.2673-0.21232.6235-2.14.86740.09370.14350.1613-0.0156-0.1380.2394-0.3419-0.00430.0443-0.14430.0157-0.0347-0.14520.0247-0.128539.80915.599812.9317
82.5418-0.3239-1.97923.4163-1.68757.53010.11340.12570.04060.0679-0.4789-0.3713-0.31280.87330.3655-0.168-0.0329-0.0598-0.00280.1315-0.057849.986120.52086.4383
95.23031.39360.09211.84853.24592.9588-0.1531-0.06910.09650.21130.0752-0.0523-0.28170.12920.07790.4053-0.4754-0.1051-0.05140.0288-0.035951.287635.37815.0935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|56 - A|77 }A56 - 77
2X-RAY DIFFRACTION2{ A|78 - A|97 }A78 - 97
3X-RAY DIFFRACTION3{ A|98 - A|129 }A98 - 129
4X-RAY DIFFRACTION4{ A|130 - A|138 }A130 - 138
5X-RAY DIFFRACTION5{ A|139 - A|177 }A139 - 177
6X-RAY DIFFRACTION6{ A|178 - A|207 }A178 - 207
7X-RAY DIFFRACTION7{ A|208 - A|229 }A208 - 229
8X-RAY DIFFRACTION8{ A|230 - A|275 }A230 - 275
9X-RAY DIFFRACTION9{ A|276 - A|289 }A276 - 289

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