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- PDB-4qlr: Llama nanobody n02 raised against EAEC T6SS TssM -

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Basic information

Entry
Database: PDB / ID: 4qlr
TitleLlama nanobody n02 raised against EAEC T6SS TssM
ComponentsLlama nanobody n02 VH domain
KeywordsIMMUNE SYSTEM / nanobody / immunoglobulin domain / T6SS TssM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionJun 13, 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 16, 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: Llama nanobody n02 VH domain
B: Llama nanobody n02 VH domain


Theoretical massNumber of molelcules
Total (without water)28,5792
Polymers28,5792
Non-polymers00
Water3,801211
1
A: Llama nanobody n02 VH domain


Theoretical massNumber of molelcules
Total (without water)14,2901
Polymers14,2901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Llama nanobody n02 VH domain


Theoretical massNumber of molelcules
Total (without water)14,2901
Polymers14,2901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 48.603, 52.872
Angle α, β, γ (deg.)90.00, 118.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Llama nanobody n02 VH domain


Mass: 14289.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.99 Å3/Da / Density % sol: 38.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES 0.1M pH 6.5, PEG 8k 30% m/v, Am2SO4 0.2M , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.071 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2014
RadiationMonochromator: high resolution Si(311) cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 23498 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.64 % / Biso Wilson estimate: 20.97 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.52 / % possible all: 90.3

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Processing

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

4hek
PDB Unreleased entry


Resolution: 1.7→44.1 Å / Cor.coef. Fo:Fc: 0.9235 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1201 5.11 %RANDOM
Rwork0.2054 ---
all0.2078 ---
obs0.2078 23496 94.65 %-
Displacement parametersBiso mean: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--5.7894 Å20 Å2-3.3774 Å2
2--7.3978 Å20 Å2
3----1.6084 Å2
Refine analyzeLuzzati coordinate error obs: 0.221 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 0 211 2141
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011985HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022695HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0635SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes039HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0305HARMONIC5
X-RAY DIFFRACTIONt_it01985HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion15.39
X-RAY DIFFRACTIONt_chiral_improper_torsion0237SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact02402SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2543 133 4.85 %
Rwork0.2397 2609 -
all0.2404 2742 -
obs--94.65 %
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)
1-0.3575-0.1640.15220.01330.05431.18080.0054-0.0036-0.00670.0261-0.0052-0.0097-0.0031-0.0054-0.00020.00360.0360.0456-0.01650.03440.01874.9725-5.92811.4917
2-0.86780.55360.94981.2806-0.18131.62910.0063-0.008-0.01040.070.01540.03870.00920.045-0.0216-0.05550.00410.0123-0.0022-0.01120.00950.42132.31799.4366
30.9787-0.015-0.52110.4251-0.21970.11420.00860.0202-0.0466-0.0091-0.04970.0312-0.00040.01870.0411-0.04860.0060.0152-0.0294-0.00160.06720.7031-4.9083-1.1578
40.783-0.8569-0.68610.44910.5259-0.1668-0.0073-0.00040.012-0.0690.0026-0.0462-0.00340.04260.0047-0.0536-0.00790.01920.00480.00560.04294.54296.4546-2.0656
5-0.15910.40990.17110.9978-0.46090.229-0.0054-0.01740.01190.04320.02580.0053-0.00360.0309-0.0204-0.03090.02890.03070.0134-0.00820.0235.49026.10710.419
60.6065-0.2409-0.01250.4556-0.124-0.1875-0.010.0037-0.014-0.0241-0.02630.02050.00160.00740.0362-0.05280.0004-0.0029-0.0418-0.00790.0816-8.26790.6612-0.4102
70.02540.09380.15280.41940.10350.2739-0.0047-0.00440.00560.0144-0.0180.0019-0.0049-0.00850.0227-0.0706-0.02710.00320.03690.03350.053914.4585-4.23273.2439
80.50980.66340.01010-0.6113-0.0901-0.034-0.00650.0051-0.01930.0184-0.01930.02620.00740.0155-0.0765-0.0060.0214-0.02180.01080.09211.7813-4.7914-2.1408
90.0890.0365-0.00870.2429-0.3099-0.0349-0.0049-0.0010.0014-0.0236-0.00360.0118-0.00430.01390.0084-0.0364-0.00290.03020.01830.01290.0095-0.1849-8.16936.3586
100.29630.4757-0.01641.0860.2228-0.10260.0029-0.00880.0024-0.00650.0018-0.0233-0.0070.021-0.0047-0.1275-0.00940.02460.00960.01650.1182-24.23530.727-0.2024
110.29390.0043-0.25530.00030.2355-0.0333-0.0055-0.0020.00480.00680.0042-0.01940.001-0.00070.00120.0025-0.03770.0522-0.0159-0.00310.0188-1.1215-5.172519.7207
120.5851-0.7016-0.50080.99130.6942-0.16890.0174-0.009-0.0034-0.0535-0.0423-0.015-0.03470.01970.02490.00370.00040.0178-0.03270.01040.0073-9.0298-12.833313.9141
130.07370.7326-0.12610.23071.10470.4085-0.0168-0.01190.01870.02780.0107-0.00330.01590.04670.0061-0.0508-0.00130.0268-0.0190.00780.0514-4.339-8.508627.2356
14-0.2029-0.63080.08210.29290.09450.4089-0.00920.00040.0206-0.0083-0.00610.0113-0.0102-0.0130.01530.0315-0.00360.0449-0.0124-0.0329-0.0154-18.2389-3.794324.0558
15-0.2059-0.02340.26760.09590.29860.3459-0.0148-0.0124-0.01710.06310.0045-0.01540.0307-0.01580.01030.0545-0.00250.0682-0.01460.0051-0.0353-10.2085-16.408530.8198
16-0.1827-0.24330.26780.8950.70520.3394-0.0179-0.00330.01140.02410.0153-0.06210.02020.01420.0026-0.01190.00160.0352-0.01780.00410.0266-5.2131-16.998222.2885
17-0.32410.53220.2680.1460.27610.61630.0144-0.0009-0.0286-0.0164-0.02330.0318-0.01410.03170.00890.00670.00480.0409-0.0334-0.00670.0309-15.8944-10.151117.5284
180.0666-0.1052-0.0010.056-0.06380.02620.0029-0.0010.00560.0072-0.00670.0016-0.00940.00750.0038-0.00490.0269-0.0037-0.00990.00910.0121-4.015-7.797636.4195
19-0.02810.23870.06250-0.03890.36340.0154-0.0042-0.01390.00720.00710.003-0.00190.0066-0.02250.0597-0.02770.0461-0.0342-0.016-0.0171-9.7364-4.270633.5518
20-0.0353-0.16640.02181.009-0.2130.04170.019-0.0227-0.0206-0.04840.00480.06930.00420.0314-0.0238-0.0116-0.00060.01960.0025-0.00770.0003-9.6288-4.008718.1983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 9}A1 - 9
2X-RAY DIFFRACTION2{A|10 - 31}A10 - 31
3X-RAY DIFFRACTION3{A|32 - 46}A32 - 46
4X-RAY DIFFRACTION4{A|47 - 70}A47 - 70
5X-RAY DIFFRACTION5{A|71 - 83}A71 - 83
6X-RAY DIFFRACTION6{A|84 - 95}A84 - 95
7X-RAY DIFFRACTION7{A|96 - 101}A96 - 101
8X-RAY DIFFRACTION8{A|102 - 113}A102 - 113
9X-RAY DIFFRACTION9{A|114 - 119}A114 - 119
10X-RAY DIFFRACTION10{A|120 - 130}A120 - 130
11X-RAY DIFFRACTION11{B|2 - 9}B2 - 9
12X-RAY DIFFRACTION12{B|10 - 26}B10 - 26
13X-RAY DIFFRACTION13{B|27 - 40}B27 - 40
14X-RAY DIFFRACTION14{B|41 - 48}B41 - 48
15X-RAY DIFFRACTION15{B|49 - 64}B49 - 64
16X-RAY DIFFRACTION16{B|65 - 83}B65 - 83
17X-RAY DIFFRACTION17{B|84 - 97}B84 - 97
18X-RAY DIFFRACTION18{B|98 - 104}B98 - 104
19X-RAY DIFFRACTION19{B|105 - 112}B105 - 112
20X-RAY DIFFRACTION20{B|113 - 123}B113 - 123

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