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- PDB-7lvu: Structure of RSV F-directed VHH Cl184 -

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Basic information

Entry
Database: PDB / ID: 7lvu
TitleStructure of RSV F-directed VHH Cl184
ComponentsF-VHH-Cl184
KeywordsIMMUNE SYSTEM / nanobody / VHH / antibody
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsHsieh, C.-L. / McLellan, J.S.
CitationJournal: J.Virol. / Year: 2021
Title: A vulnerable, membrane-proximal site in human respiratory syncytial virus F revealed by a prefusion-specific single-domain antibody.
Authors: Rossey, I. / Hsieh, C.L. / Sedeyn, K. / Ballegeer, M. / Schepens, B. / Mclellan, J.S. / Saelens, X.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F-VHH-Cl184
B: F-VHH-Cl184
C: F-VHH-Cl184
D: F-VHH-Cl184


Theoretical massNumber of molelcules
Total (without water)67,6044
Polymers67,6044
Non-polymers00
Water6,377354
1
A: F-VHH-Cl184


Theoretical massNumber of molelcules
Total (without water)16,9011
Polymers16,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F-VHH-Cl184


Theoretical massNumber of molelcules
Total (without water)16,9011
Polymers16,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: F-VHH-Cl184


Theoretical massNumber of molelcules
Total (without water)16,9011
Polymers16,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: F-VHH-Cl184


Theoretical massNumber of molelcules
Total (without water)16,9011
Polymers16,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.600, 73.600, 221.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-289-

HOH

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Components

#1: Antibody
F-VHH-Cl184


Mass: 16900.924 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): FreeStyle293 / Production host: Homo sapiens (human)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 2.0 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.94→73.9 Å / Num. obs: 46193 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.998 / Net I/σ(I): 17.1
Reflection shellResolution: 1.94→1.99 Å / Num. unique obs: 2987 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAK

5vak


Resolution: 1.94→73.6 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2267 4.92 %
Rwork0.2075 43832 -
obs0.2088 46099 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.88 Å2 / Biso mean: 30.2735 Å2 / Biso min: 14.12 Å2
Refinement stepCycle: final / Resolution: 1.94→73.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 0 354 4084
Biso mean---36.92 -
Num. residues----490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.94-1.980.28571550.26992615277098
1.98-2.030.29371520.25742640279299
2.03-2.080.27511300.251327022832100
2.08-2.140.24311440.231626852829100
2.14-2.20.27651310.236226922823100
2.2-2.270.21751460.239927102856100
2.27-2.350.25781350.231127152850100
2.35-2.450.31791440.242127092853100
2.45-2.560.27981340.236727332867100
2.56-2.690.22761400.230327112851100
2.69-2.860.26291290.220127532882100
2.86-3.080.24211180.213427802898100
3.08-3.390.21181500.202827522902100
3.39-3.880.20621780.17727732951100
3.88-4.890.18681390.156628362975100
4.89-73.60.22681420.201930263168100
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)
12.81350.8507-1.17822.5472-0.32473.76710.0732-0.16250.17880.0383-0.0256-0.1077-0.14940.4213-0.00670.0715-0.01440.00410.0964-0.02250.1287-30.63713.232-14.884
22.7807-0.4988-0.35023.8510.08984.7534-0.0257-0.22280.11340.10880.17440.0198-0.29860.2502-0.05110.127-0.0455-0.00660.1792-0.0430.1181-10.612-13.093-16.816
33.9045-0.95321.29282.39130.55113.56330.23070.3961-0.1139-0.2836-0.13360.03240.06810.119-0.05140.28640.03750.02630.1383-0.03260.1477-32.0433.456-39.978
42.5158-0.671-1.80033.86381.19024.4140.045-0.27440.3364-0.37570.1825-0.1623-0.93170.775-0.03760.3205-0.20680.02080.2544-0.05280.197-4.85-14.662-43.395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:113 )A2 - 113
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:113 )B1 - 113
3X-RAY DIFFRACTION3( CHAIN C AND RESID 2:113 )C2 - 113
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:113 )D1 - 113

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