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- PDB-5lmw: Llama nanobody PorM_02 -

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Basic information

Entry
Database: PDB / ID: 5lmw
TitleLlama nanobody PorM_02
ComponentsNanobody
KeywordsIMMUNE SYSTEM / NANOBODY / PORPHYROMONAS GINGIVALIS / TYPE 9 SECRETION SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRoche, J. / Gaubert, A. / 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
DepositionAug 1, 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 1.4Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.5Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6102
Polymers14,5181
Non-polymers921
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-0 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.680, 65.680, 88.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Nanobody


Mass: 14518.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6 / Cell (production host): WK6 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Tri-sodium Citrate PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 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: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.5→46.44 Å / Num. obs: 31805 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.68 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.627 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y7M

4y7m


Resolution: 1.5→19.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.062 / SU Rfree Cruickshank DPI: 0.056
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1592 5.02 %RANDOM
Rwork0.188 ---
obs0.188 31733 99.9 %-
Displacement parametersBiso mean: 30.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.0936 Å20 Å20 Å2
2--3.0936 Å20 Å2
3----6.1872 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.5→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 6 213 1153
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01978HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.981321HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d344SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes22HARMONIC2
X-RAY DIFFRACTIONt_gen_planes149HARMONIC5
X-RAY DIFFRACTIONt_it978HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.43
X-RAY DIFFRACTIONt_other_torsion14.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion119SEMIHARMONIC5
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_contact1199SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.216 143 5.02 %
Rwork0.218 2708 -
all0.218 2851 -
obs--99.48 %
Refinement TLS params.Method: refined / Origin x: 4.5416 Å / Origin y: -19.3186 Å / Origin z: 9.4822 Å
111213212223313233
T-0.0727 Å20.0062 Å2-0.0093 Å2--0.0048 Å20.0108 Å2---0.0001 Å2
L2.0951 °20.6078 °20.4695 °2-1.1975 °20.0095 °2--0.7778 °2
S-0.0221 Å °0.1178 Å °-0.0094 Å °-0.0573 Å °0.0287 Å °-0.0116 Å °0.0339 Å °-0.0196 Å °-0.0065 Å °
Refinement TLS groupSelection details: { A|* }

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