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- PDB-6ey0: N-terminal part (residues 30-212) of PorM with the llama nanobody nb01 -

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Basic information

Entry
Database: PDB / ID: 6ey0
TitleN-terminal part (residues 30-212) of PorM with the llama nanobody nb01
Components
  • (llama nanobody nb01) x 2
  • T9SS component cytoplasmic membrane protein PorM
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: 2.4 Å
AuthorsLeone, P. / Roche, J. / 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: Source and taxonomy / Structure summary / Category: entity_src_gen / struct
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _struct.title
Revision 1.3Jan 17, 2024Group: 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
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: llama nanobody nb01
F: llama nanobody nb01
G: llama nanobody nb01
H: llama nanobody nb01


Theoretical massNumber of molelcules
Total (without water)148,1328
Polymers148,1328
Non-polymers00
Water2,846158
1
A: T9SS component cytoplasmic membrane protein PorM
E: llama nanobody nb01


Theoretical massNumber of molelcules
Total (without water)36,9752
Polymers36,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T9SS component cytoplasmic membrane protein PorM
F: llama nanobody nb01


Theoretical massNumber of molelcules
Total (without water)37,2062
Polymers37,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: T9SS component cytoplasmic membrane protein PorM
G: llama nanobody nb01


Theoretical massNumber of molelcules
Total (without water)36,9752
Polymers36,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: T9SS component cytoplasmic membrane protein PorM
H: llama nanobody nb01


Theoretical massNumber of molelcules
Total (without water)36,9752
Polymers36,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.283, 99.924, 80.291
Angle α, β, γ (deg.)90.00, 93.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
T9SS component cytoplasmic membrane protein PorM


Mass: 21979.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: residue Glu145 is mutated to Asp / Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: porM, PGIN_15-9_01458 / Plasmid: pET28a derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A1R4DSC1, UniProt: B2RLE8*PLUS
#2: Antibody llama nanobody nb01


Mass: 14995.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Antibody llama nanobody nb01


Mass: 15225.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M bis-tris pH 7.0, 25%(w/v) PEG 3350

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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 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→42.47 Å / Num. obs: 49059 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 67.23 Å2 / Rrim(I) all: 0.078 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 7020 / CC1/2: 0.755 / Rpim(I) all: 0.774 / Rrim(I) all: 2.033 / % possible all: 96.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lz0

5lz0


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.406 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2456 5.03 %RANDOM
Rwork0.213 ---
obs0.214 48833 98.5 %-
Displacement parametersBiso mean: 120.65 Å2
Baniso -1Baniso -2Baniso -3
1--8.5867 Å20 Å2-33.8604 Å2
2--1.0987 Å20 Å2
3---7.4881 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8571 0 0 158 8729
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098710HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1211748HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3123SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes217HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1259HARMONIC5
X-RAY DIFFRACTIONt_it8710HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion17.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1122SEMIHARMONIC5
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_contact9854SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 198 5.52 %
Rwork0.216 3391 -
all0.219 3589 -
obs--97.91 %
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)
15.3372.8929-3.26954.8987-2.68286.7307-0.4205-0.4803-0.42910.2706-0.0679-0.64550.19930.64310.4885-0.24580.0813-0.0671-0.2454-0.018-0.2878-31.7021-28.391223.1813
24.35240.7201-0.77645.44063.27547.3699-0.3198-0.4906-0.04590.9994-0.38280.371.26480.0190.7025-0.14140.15590.3238-0.33820.1202-0.3128-47.0016-2.784342.7583
34.3369-1.7281-1.03855.0895-1.7164.2164-0.05070.46320.1341-0.9193-0.0265-0.27660.5265-0.18050.0773-0.0304-0.19340.3376-0.4115-0.1059-0.1909-0.05982.042338.1523
45.22621.3013-4.03714.4945-2.18117.6341-0.2919-0.5301-0.26620.6497-0.0976-0.37870.2280.70320.3895-0.09150.0759-0.012-0.39630.0311-0.19518.776924.205723.1513
58.5364-3.76434.86343.12490.08165.1959-0.10461.59680.673-1.2142-0.18320.5410.1857-1.24980.2879-0.2404-0.337-0.35930.3420.1339-0.5158-44.3813-20.4158-1.0451
69.0540.5603-7.21011.69670.194410.12310.26030.94450.5467-0.010.22570.108-0.6377-0.5814-0.486-0.23440.14950.1153-0.18120.1693-0.322-34.66691.652516.2081
75.67270.398-5.45962.3879-0.623410.58070.0666-0.27660.24890.04290.3275-0.0612-0.4089-0.1948-0.3941-0.1722-0.01850.1345-0.2033-0.0879-0.2026-13.21073.973564.5983
84.5388-0.98441.76952.94530.82126.7715-0.19990.90930.4411-1.1807-0.57480.9336-0.9183-1.63290.7747-0.10390.1916-0.38740.0058-0.1631-0.3049-4.041931.9604-0.9691
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|* }

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