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- PDB-4qgy: Camelid (llama) nanobody n25 (VHH) against type 6 secretion syste... -

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Basic information

Entry
Database: PDB / ID: 4qgy
TitleCamelid (llama) nanobody n25 (VHH) against type 6 secretion system TssM protein
Componentsnanobody n25, VH domain
KeywordsIMMUNE SYSTEM / immunoglobulin domain / protein recognition / T6SS TssM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsNguyen, V.S. / Desmyter, A. / Le, T.T.H. / Durand, E. / Kellenberger, C. / Douzi, B. / Spinelli, S. / Cascales, E. / Cambillau, C. / Roussel, A.
CitationJournal: Plos One / Year: 2015
Title: Inhibition of Type VI Secretion by an Anti-TssM Llama Nanobody.
Authors: Nguyen, V.S. / Logger, L. / Spinelli, S. / Desmyter, A. / Le, T.T. / Kellenberger, C. / Douzi, B. / Durand, E. / Roussel, A. / Cascales, E. / Cambillau, C.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nanobody n25, VH domain
B: nanobody n25, VH domain


Theoretical massNumber of molelcules
Total (without water)29,4532
Polymers29,4532
Non-polymers00
Water5,567309
1
A: nanobody n25, VH domain


Theoretical massNumber of molelcules
Total (without water)14,7261
Polymers14,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: nanobody n25, VH domain


Theoretical massNumber of molelcules
Total (without water)14,7261
Polymers14,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.980, 70.950, 145.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody nanobody n25, VH domain


Mass: 14726.342 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) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: KNa Tartrate 1.2M, CHES 0.1M, Li2SO4 0.2M, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2014
RadiationMonochromator: Kirkpatrick-Baez pair of bi-morph mirrors, channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. all: 55440 / Num. obs: 55440 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 20.27 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 28.7
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.63 / Num. unique all: 3886 / % possible all: 95

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HEP

4hep


Resolution: 1.38→20.15 Å / Cor.coef. Fo:Fc: 0.9606 / Cor.coef. Fo:Fc free: 0.9632 / SU R Cruickshank DPI: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 2813 5.08 %RANDOM
Rwork0.1911 ---
all0.1915 55416 --
obs0.1915 55416 99.52 %-
Displacement parametersBiso mean: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.4628 Å20 Å20 Å2
2---3.7302 Å20 Å2
3---2.2674 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 1.38→20.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 309 2218
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011967HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092678HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0622SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes039HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0302HARMONIC5
X-RAY DIFFRACTIONt_it01967HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.85
X-RAY DIFFRACTIONt_other_torsion13.74
X-RAY DIFFRACTIONt_chiral_improper_torsion0254SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact02490SEMIHARMONIC4
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3671 187 4.9 %
Rwork0.3199 3627 -
all0.3221 3814 -
obs-3886 99.52 %
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)
10.0276-0.0371-0.00030.0441-0.0030.0190.0001-0.0001-0.00060.0003-0.00020.0015-0.0025-0.00110-0.0051-0.0222-0.0013-0.00580.00610.01119.333432.2886-14.791
20.1565-0.2327-0.46210.0517-0.19310.25920.00130.01050.0067-0.0141-0.0257-0.01780.00930.00120.0244-0.0189-0.0346-0.00750.01040.01580.00246.295322.2225-16.1628
30.0476-0.05030.07150.0001-0.05350.105-0.0004-0.005-0.00080.0010.0024-0.00160.0004-0.0023-0.002-0.0092-0.02-0.00070.03280.0166-0.02252.598720.8014-0.9016
40.2219-0.13510.23050.09-0.07070.0650.0013-0.0033-0.0111-0.00520.0027-0.00040.00660.0172-0.004-0.0144-0.0226-0.0012-0.00210.03190.018711.022613.008-12.0657
50.1626-0.11260.04430.2180.21030.11790.00290.007-0.0024-0.01-0.0116-0.00380.0034-0.00280.00870.0012-0.02830.009-0.0040.00920.00073.892717.345-17.041
60.5007-0.203-0.210.21980.00340.3657-0.0031-0.00810.01620.0282-0.012-0.01960.01850.02740.0151-0.0258-0.0186-0.00990.00930.02190.00076.168521.1656-7.95
70.0068-0.1818-0.10440.3147-0.2680.4360.0012-0.01720.0029-0.0187-0.00110.00310.02510.010500.0024-0.034-0.0144-0.0119-0.00130.0014-13.09866.2285-24.748
80.06690.2250.07280.01610.09890.3141-0.00240.0008-0.0029-0.0201-0.008-0.00780.0042-0.01430.01050.0223-0.0199-0.0102-0.01290.0102-0.0148-13.173711.1054-34.6676
90.310.0076-0.13140.08740.13980.15460.0033-0.0073-0.012-0.0130.0032-0.005-0.00120.0112-0.00650.0123-0.02390.0236-0.01020.0175-0.0034-5.79299.7213-28.2531
100.00390.01530.37630.0196-0.19070.33150.00210.00530.0115-0.0079-0.0009-0.00360.0003-0.0097-0.00120.0048-0.0247-0.0274-0.00020.0065-0.008-15.296415.69-28.7565
1100.01220.006400.00190.01010.00010.0008-0.00040.0005-0.00030.00070.0001-0.00040.00020.0052-0.00240.0002-0.0022-0.0011-0.0014-14.21713.2574-42.2478
120.14440.10310.27970.1964-0.25720.23360.00570.00230.0114-0.00690.00030.00720.0009-0.0066-0.0061-0.0027-0.0326-0.04830.0037-0.0027-0.009-18.68912.0856-30.3397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 36
3X-RAY DIFFRACTION3A37 - 46
4X-RAY DIFFRACTION4A47 - 72
5X-RAY DIFFRACTION5A73 - 89
6X-RAY DIFFRACTION6A90 - 135
7X-RAY DIFFRACTION7B1 - 33
8X-RAY DIFFRACTION8B34 - 62
9X-RAY DIFFRACTION9B63 - 86
10X-RAY DIFFRACTION10B87 - 99
11X-RAY DIFFRACTION11B100 - 109
12X-RAY DIFFRACTION12B110 - 129

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