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- PDB-6ey6: C-terminal part (residues 315-516) of PorM with the llama nanobod... -

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Basic information

Entry
Database: PDB / ID: 6ey6
TitleC-terminal part (residues 315-516) of PorM with the llama nanobody nb130
Components
  • T9SS component cytoplasmic membrane protein PorM
  • nb130
KeywordsPROTEIN TRANSPORT / Type IV Secretion System (T9SS) / nanobody
Function / homology
Function and homology information


: / : / GldM second domain / GldM third domain / Gliding motility-associated protein GldM / Gliding motility-associated protein GldM, C-terminal / Gliding motility-associated protein GldM, N-terminal / GldM C-terminal domain / GldM N-terminal domain
Similarity search - Domain/homology
: / Por secretion system protein porM/gldM
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLeone, P. / Cambillau, C. / Roussel, A.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0019-01 France
French Infrastructure for Integrated Structural Biology France
Citation
Journal: Nat Commun / Year: 2018
Title: Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space.
Authors: Leone, P. / Roche, J. / Vincent, M.S. / Tran, Q.H. / Desmyter, A. / Cascales, E. / Kellenberger, C. / Cambillau, C. / Roussel, A.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis.
Authors: Duhoo, Y. / Roche, J. / Trinh, T.T.N. / Desmyter, A. / Gaubert, A. / Kellenberger, C. / Cambillau, C. / Roussel, A. / Leone, P.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T9SS component cytoplasmic membrane protein PorM
B: T9SS component cytoplasmic membrane protein PorM
C: T9SS component cytoplasmic membrane protein PorM
D: T9SS component cytoplasmic membrane protein PorM
E: T9SS component cytoplasmic membrane protein PorM
F: T9SS component cytoplasmic membrane protein PorM
G: T9SS component cytoplasmic membrane protein PorM
H: T9SS component cytoplasmic membrane protein PorM
I: nb130
J: nb130
K: nb130
L: nb130
M: nb130
N: nb130
O: nb130
P: nb130


Theoretical massNumber of molelcules
Total (without water)395,46216
Polymers395,46216
Non-polymers00
Water22,2491235
1
A: T9SS component cytoplasmic membrane protein PorM
B: T9SS component cytoplasmic membrane protein PorM
I: nb130
J: nb130


Theoretical massNumber of molelcules
Total (without water)98,8664
Polymers98,8664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T9SS component cytoplasmic membrane protein PorM
D: T9SS component cytoplasmic membrane protein PorM
K: nb130
L: nb130


Theoretical massNumber of molelcules
Total (without water)98,8664
Polymers98,8664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: T9SS component cytoplasmic membrane protein PorM
F: T9SS component cytoplasmic membrane protein PorM
M: nb130
N: nb130


Theoretical massNumber of molelcules
Total (without water)98,8664
Polymers98,8664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: T9SS component cytoplasmic membrane protein PorM
H: T9SS component cytoplasmic membrane protein PorM
O: nb130
P: nb130


Theoretical massNumber of molelcules
Total (without water)98,8664
Polymers98,8664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.245, 77.179, 156.302
Angle α, β, γ (deg.)90.24, 91.76, 97.16
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
T9SS component cytoplasmic membrane protein PorM


Mass: 34367.082 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: porM, PGIN_15-9_01458 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R4DSC1, UniProt: B2RLE8*PLUS
#2: Antibody
nb130


Mass: 15065.688 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1235 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium citrate tribasic pH 7.0 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 145898 / % possible obs: 97.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 43.18 Å2 / Rrim(I) all: 0.065 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 221179 / CC1/2: 0.647 / Rpim(I) all: 0.433 / Rrim(I) all: 0.764 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EY5, 5FWO

6ey5

5fwo


Resolution: 2.1→38.35 Å / Cor.coef. Fo:Fc: 0.9559 / Cor.coef. Fo:Fc free: 0.9404 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 7242 4.98 %RANDOM
Rwork0.1806 ---
obs0.1823 145522 97.37 %-
Displacement parametersBiso mean: 53.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.3958 Å25.7393 Å21.0797 Å2
2---6.2532 Å2-0.2692 Å2
3---4.8575 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: 1 / Resolution: 2.1→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19361 0 0 1236 20597
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0120527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1327754HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7156SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes477HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3037HARMONIC5
X-RAY DIFFRACTIONt_it20527HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion16.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2693SEMIHARMONIC5
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_contact22733SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2361 499 4.83 %
Rwork0.2112 9828 -
all0.2123 10327 -
obs--93.54 %
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)
10.9060.1138-0.23640.9765-0.51731.90770.01650.1512-0.11910.01410.0580.0108-0.18680.0315-0.0745-0.141-0.0294-0.009-0.1274-0.0014-0.13-6.0579-2.3465-74.7948
21.45390.2313-0.03521.427-0.2032.12390.06320.02130.18970.1992-0.032-0.071-0.20810.276-0.0312-0.1655-0.10260.0029-0.168-0.0209-0.2118.335310.3296-73.1064
31.06510.4381-0.17120.7683-0.28433.20970.08560.0154-0.19910.07360.0633-0.03090.0402-0.0083-0.1489-0.14270.0197-0.0111-0.16830.0031-0.0908-10.172534.1776-37.4862
41.55260.73880.12131.08850.57141.07170.1298-0.05450.03360.1636-0.0719-0.02680.13410.0074-0.0579-0.15470.010.0247-0.168-0.0111-0.15373.42647.4664-36.2957
51.31840.3196-0.07141.50710.64022.14570.0450.0302-0.17540.2365-0.10590.08990.1014-0.18640.0609-0.1707-0.0602-0.0082-0.11460.005-0.2018-7.9779-5.29874.1633
61.10240.13430.28811.15261.01712.1071-0.01670.16640.110.04780.1389-0.02150.11970.1202-0.1221-0.1798-0.03210.0057-0.1405-0.0037-0.13636.60757.3943.9244
71.62560.3232-0.55711.39510.0192.03030.17550.1004-0.29060.079-0.0796-0.0138-0.0394-0.0043-0.0959-0.18520.0187-0.0746-0.1733-0.001-0.1564-14.349333.819141.8629
81.32790.26270.26620.68720.68723.1650.10420.12050.2162-0.0192-0.0150.02580.04650.0213-0.0892-0.14720.030.0163-0.1570.0243-0.1558-0.93147.000740.9434
93.7211-1.3711.21564.513-0.91141.616-0.12770.10430.04030.41990.11630.6509-0.0613-0.06510.0114-0.1017-0.0570.0405-0.13190.0681-0.0522-23.282620.1062-82.2658
103.0666-0.08790.51512.07440.29321.051-0.00620.1201-0.19250.1947-0.0176-0.14280.10050.1060.0238-0.1321-0.0430.00240.0155-0.0154-0.146125.6435-10.1873-81.2911
113.0358-0.1785-0.47060.8608-0.3451.33230.00670.0680.15290.1164-0.04270.0464-0.03350.01370.036-0.0739-0.0001-0.0058-0.09510.0064-0.0727-27.782455.7931-42.5168
125.4853-1.3453-0.1581.14050.50191.0269-0.06180.242-0.63560.1524-0.07220.08570.1179-0.02490.134-0.13390.01040.032-0.1786-0.0110.038121.708926.7907-45.5152
133.2461-1.17470.58016.0325-2.11681.5817-0.05080.14910.02160.38360.55671.2711-0.0576-0.1943-0.506-0.2124-0.01740.0842-0.11510.18630.0792-24.380115.7557-5.0933
144.2176-0.25930.54051.88840.46361.3676-0.02670.0628-0.27710.21090.0134-0.14340.10240.11950.0132-0.1599-0.02980-0.0036-0.0375-0.132224.751-14.4953-2.3928
155.466-1.03140.36690.8364-0.6531.4931-0.05980.42330.73260.1477-0.0331-0.026-0.11870.02440.0929-0.14780.0198-0.0296-0.17230.04090.0327-32.150254.614532.6267
163.0895-0.03610.58331.51140.0041.3150.01890.1086-0.27140.1794-0.0522-0.09670.03580.0280.0333-0.09140.0374-0.0268-0.1028-0.0236-0.079317.326225.660636.002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }
13X-RAY DIFFRACTION13{ M|* }
14X-RAY DIFFRACTION14{ N|* }
15X-RAY DIFFRACTION15{ O|* }
16X-RAY DIFFRACTION16{ P|* }

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