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- PDB-5lz0: Llama nanobody PorM_01 -

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Basic information

Entry
Database: PDB / ID: 5lz0
TitleLlama nanobody PorM_01
ComponentsPorM nanobody
KeywordsIMMUNE SYSTEM / nanobody / Porphyromonas gingivalis / Type-9 Secretion System (T9SS)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDuhoo, Y. / Leone, P. / Roussel, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: 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
DepositionSep 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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

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Assembly

Deposited unit
A: PorM nanobody
B: PorM nanobody


Theoretical massNumber of molelcules
Total (without water)29,9912
Polymers29,9912
Non-polymers00
Water4,522251
1
A: PorM nanobody


Theoretical massNumber of molelcules
Total (without water)14,9961
Polymers14,9961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PorM nanobody


Theoretical massNumber of molelcules
Total (without water)14,9961
Polymers14,9961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.327, 65.828, 48.314
Angle α, β, γ (deg.)90.00, 95.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-279-

HOH

21B-321-

HOH

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Components

#1: Antibody PorM nanobody


Mass: 14995.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0,1M Tri-Sodium Citrate 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→28.8 Å / Num. obs: 31426 / % possible obs: 97.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 19.47 Å2 / Net I/σ(I): 10.5
Reflection shellResolution: 1.6→1.69 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVS

4tvs


Resolution: 1.6→27.16 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.106 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1584 5.04 %RANDOM
Rwork0.203 ---
obs0.205 31426 97.5 %-
Displacement parametersBiso mean: 22.78 Å2
Baniso -1Baniso -2Baniso -3
1--5.184 Å20 Å2-1.5059 Å2
2---1.4819 Å20 Å2
3---6.6659 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.6→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 0 251 2153
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011943HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d652SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes295HARMONIC5
X-RAY DIFFRACTIONt_it1943HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion13.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
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_contact2349SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.257 125 4.6 %
Rwork0.233 2591 -
all0.234 2716 -
obs--92.01 %

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