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- PDB-6gzp: Llama nanobody PorM_02 structure determined at room temperature b... -

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Basic information

Entry
Database: PDB / ID: 6gzp
TitleLlama nanobody PorM_02 structure determined at room temperature by in-situ diffraction in ChipX microfluidic device
ComponentsNanobody
KeywordsIMMUNE SYSTEM / Llama nanobody / Porphyromonas gingivalis / PorM
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoche, J. / Gaubert, A. / Desmyter, A. / De Wijn, R. / Sauter, C. / Roussel, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Iucrj / Year: 2019
Title: A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.
Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. ...Authors: de Wijn, R. / Hennig, O. / Roche, J. / Engilberge, S. / Rollet, K. / Fernandez-Millan, P. / Brillet, K. / Betat, H. / Morl, M. / Roussel, A. / Girard, E. / Mueller-Dieckmann, C. / Fox, G.C. / Olieric, V. / Gavira, J.A. / Lorber, B. / Sauter, C.
History
DepositionJul 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _exptl_crystal_grow.pdbx_details / _struct.title
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 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 1.4Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)14,5181
Polymers14,5181
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.680, 66.680, 91.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

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Components

#1: Antibody Nanobody / Llama nanobody PorM_02


Mass: 14518.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 293.15 K / Method: microfluidic
Details: Tri-sodium Citrate PEG 3000. ChipX microfluidic device

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.826561272144 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826561272144 Å / Relative weight: 1
ReflectionResolution: 2.1→41.9432 Å / Num. obs: 12281 / % possible obs: 97.14 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.037 / Rrim(I) all: 0.075 / Net I/σ(I): 1.8
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.731 / Rpim(I) all: 0.421 / Rrim(I) all: 0.847

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LMW

5lmw


Resolution: 2.1→41.943 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2108 --
Rwork0.1685 --
obs0.1727 12276 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 23 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008977
X-RAY DIFFRACTIONf_angle_d0.8971321
X-RAY DIFFRACTIONf_dihedral_angle_d2.509779
X-RAY DIFFRACTIONf_chiral_restr0.052137
X-RAY DIFFRACTIONf_plane_restr0.004172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.18430.30651340.26431206X-RAY DIFFRACTION98
2.1843-2.28370.26241330.24861198X-RAY DIFFRACTION98
2.2837-2.40410.27941360.24491222X-RAY DIFFRACTION98
2.4041-2.55470.28451350.22651218X-RAY DIFFRACTION98
2.5547-2.75190.25311340.21591206X-RAY DIFFRACTION97
2.7519-3.02870.26211340.20591207X-RAY DIFFRACTION96
3.0287-3.46680.23711380.18051230X-RAY DIFFRACTION97
3.4668-4.36710.17371370.12971245X-RAY DIFFRACTION96
4.3671-41.95150.16031470.13141316X-RAY DIFFRACTION96
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)
18.02053.8013.15013.52154.13535.0033-0.46730.36170.3622-1.39120.03210.588-0.3256-0.27010.3780.35120.0187-0.07070.5681-0.00530.3052-1.5199-15.7753.3397
25.58865.2468-3.0355.4363-2.63272.01130.02381.7822-0.93950.14540.8981-0.69840.48030.1303-0.93980.5601-0.0577-0.17690.6344-0.15990.6739-3.9887-32.96833.157
34.4955.657-0.48437.6909-2.69947.2852-0.65041.1143-0.3479-0.50160.8988-1.13060.29750.2575-0.33120.4385-0.0095-0.07430.60560.02540.45434.6478-16.44051.5464
42.6787-2.92331.72723.8768-4.1538.6531-0.01780.44140.3429-0.7865-0.3078-0.8495-0.060.43290.20610.3810.00050.0610.58080.15480.564415.3923-7.15444.6917
56.07233.5257-1.38219.5781-2.68744.6406-0.06780.57110.5973-0.26150.07860.23650.0255-0.38020.00740.30790.0209-0.06660.4615-0.02360.40687.4844-15.967311.3158
63.44484.0663-3.13945.042-3.7933.28210.7103-0.71121.5440.87430.35460.81130.2492-0.3639-0.91820.4189-0.00770.03090.6677-0.02310.5742-5.9726-21.166920.0156
75.951-5.6008-6.47416.01366.80097.6460.3792-0.1784-0.17370.5514-0.0846-0.3943-0.1518-0.4688-0.34290.36870.00020.030.4613-0.02150.3713.4342-20.167216.9241
82.09942.2442-0.85129.4421-1.3543.76780.45450.52930.80880.2706-0.3683-0.2013-0.1435-0.0538-0.06160.3414-0.01370.02620.5931-0.03830.461217.8917-16.568310.0536
93.81351.36742.92534.56780.35013.30240.40350.347-1.78660.3735-0.0803-2.01221.19080.7041-0.21930.4990.1349-0.09910.6235-0.07650.665614.4719-24.028912.806
107.8146-3.09244.982.3032-0.28855.74121.6218-0.2137-4.06323.10460.0584-0.24873.93170.5199-1.30811.18610.1017-0.23770.6675-0.02881.03877.6438-31.387816.0879
118.8064.18810.13739.60843.0683.6998-0.1039-0.018-1.022-0.0037-0.016-0.7431.07880.6406-0.17970.56050.0384-0.08290.3955-0.09710.5267.5394-27.48428.1809
126.9371-3.5815-0.57675.6109-3.99394.9264-0.04821.52640.5822-0.9514-0.2395-0.40730.54740.21410.30120.45120.00470.06840.78390.0180.419714.2041-15.214-0.8535
139.45126.1519-0.97378.1363-5.21545.4656-0.27731.4889-0.6594-0.62670.1178-1.42790.14260.16160.16180.48010.0096-0.07190.6961-0.04830.49698.5002-17.69631.9469
145.24973.7501-3.58313.4087-1.9513.38680.14290.2272-1.3109-0.2570.054-0.34960.75450.0235-0.23370.4784-0.0071-0.12170.5983-0.07820.62971.2003-31.44367.0116
159.33963.0014-0.3188.58530.53878.0175-0.2670.1334-0.18980.380.86820.51670.6677-0.9115-0.45540.3508-0.0814-0.07720.51750.01890.3657-4.8606-26.030112.2299
161.20060.52112.34855.60542.21034.9138-0.7554-0.10460.6543-0.79870.1221-0.0995-0.851-0.01210.32650.4376-0.0016-0.0380.51840.04650.46767.7025-11.186511.8693
174.44785.1495-0.05167.742.97785.70990.0355-1.1853-0.5571-0.57780.0533-0.6282-0.02840.4214-0.06040.33410.0216-0.06740.5306-0.07290.543214.3065-13.367718.841
185.2127-2.1961-4.31726.52542.73767.6312-0.0050.6979-0.2922-0.4643-0.0617-0.4094-0.3060.14660.03730.34960.0428-0.06040.3771-0.0050.46357.4123-10.953918.6336
192.24982.60462.28335.32415.17875.0405-0.52080.47931.974-0.27520.01811.6735-0.1727-0.51340.57090.47820.0868-0.07290.53730.02520.52561.5597-9.263410.8408
207.41864.7248-4.62665.6914-5.8176.0833-0.68910.1076-0.1471-1.59440.86140.61311.0969-1.3091-0.26730.5209-0.1476-0.15760.85680.05110.4931-8.563-26.22447.5182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:12)
2X-RAY DIFFRACTION2(chain A and resid 13:18)
3X-RAY DIFFRACTION3(chain A and resid 19:25)
4X-RAY DIFFRACTION4(chain A and resid 26:31)
5X-RAY DIFFRACTION5(chain A and resid 32:38)
6X-RAY DIFFRACTION6(chain A and resid 39:44)
7X-RAY DIFFRACTION7(chain A and resid 45:49)
8X-RAY DIFFRACTION8(chain A and resid 50:54)
9X-RAY DIFFRACTION9(chain A and resid 55:59)
10X-RAY DIFFRACTION10(chain A and resid 60:65)
11X-RAY DIFFRACTION11(chain A and resid 66:70)
12X-RAY DIFFRACTION12(chain A and resid 71:75)
13X-RAY DIFFRACTION13(chain A and resid 76:80)
14X-RAY DIFFRACTION14(chain A and resid 81:83)
15X-RAY DIFFRACTION15(chain A and resid 84:90)
16X-RAY DIFFRACTION16(chain A and resid 91:96)
17X-RAY DIFFRACTION17(chain A and resid 97:100)
18X-RAY DIFFRACTION18(chain A and resid 100A:101)
19X-RAY DIFFRACTION19(chain A and resid 102:106)
20X-RAY DIFFRACTION20(chain A and resid 107:113)

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