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- PDB-6obz: Crystal structure of FluA-20 Fab -

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Basic information

Entry
Database: PDB / ID: 6obz
TitleCrystal structure of FluA-20 Fab
Components
  • Heavy chain of FluA-20 Fab
  • Light chain of FluA-20 Fab, Immunoglobulin light chain
KeywordsIMMUNE SYSTEM / anti-flu antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsWilson, I.A. / Lang, S.
CitationJournal: Cell / Year: 2019
Title: A Site of Vulnerability on the Influenza Virus Hemagglutinin Head Domain Trimer Interface.
Authors: Bangaru, S. / Lang, S. / Schotsaert, M. / Vanderven, H.A. / Zhu, X. / Kose, N. / Bombardi, R. / Finn, J.A. / Kent, S.J. / Gilchuk, P. / Gilchuk, I. / Turner, H.L. / Garcia-Sastre, A. / Li, S. ...Authors: Bangaru, S. / Lang, S. / Schotsaert, M. / Vanderven, H.A. / Zhu, X. / Kose, N. / Bombardi, R. / Finn, J.A. / Kent, S.J. / Gilchuk, P. / Gilchuk, I. / Turner, H.L. / Garcia-Sastre, A. / Li, S. / Ward, A.B. / Wilson, I.A. / Crowe Jr., J.E.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of FluA-20 Fab
B: Light chain of FluA-20 Fab, Immunoglobulin light chain
H: Heavy chain of FluA-20 Fab
L: Light chain of FluA-20 Fab, Immunoglobulin light chain


Theoretical massNumber of molelcules
Total (without water)97,3244
Polymers97,3244
Non-polymers00
Water18,7361040
1
A: Heavy chain of FluA-20 Fab
B: Light chain of FluA-20 Fab, Immunoglobulin light chain


Theoretical massNumber of molelcules
Total (without water)48,6622
Polymers48,6622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-25 kcal/mol
Surface area19610 Å2
MethodPISA
2
H: Heavy chain of FluA-20 Fab
L: Light chain of FluA-20 Fab, Immunoglobulin light chain


Theoretical massNumber of molelcules
Total (without water)48,6622
Polymers48,6622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-25 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.577, 52.643, 104.786
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Heavy chain of FluA-20 Fab


Mass: 25154.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain of FluA-20 Fab, Immunoglobulin light chain


Mass: 23508.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-sodium citrate 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 92959 / % possible obs: 97.8 % / Redundancy: 3.5 % / CC1/2: 1 / Rpim(I) all: 0.05 / Rsym value: 0.1 / Net I/σ(I): 11.8
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.2 % / Num. unique obs: 4414 / CC1/2: 0.84 / Rpim(I) all: 0.21 / Rsym value: 0.39 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMT, 5BV7

4kmt

5bv7


Resolution: 1.73→50 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2381 4546 4.89 %
Rwork0.2021 --
obs0.2039 92945 96.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6616 0 0 1041 7657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076780
X-RAY DIFFRACTIONf_angle_d0.9299244
X-RAY DIFFRACTIONf_dihedral_angle_d13.1584070
X-RAY DIFFRACTIONf_chiral_restr0.0591052
X-RAY DIFFRACTIONf_plane_restr0.0061180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7243-1.74390.3549810.30311671X-RAY DIFFRACTION55
1.7439-1.76440.30351540.26992849X-RAY DIFFRACTION95
1.7644-1.7860.29521330.26922918X-RAY DIFFRACTION96
1.786-1.80860.34161440.24482944X-RAY DIFFRACTION96
1.8086-1.83240.29751270.22922945X-RAY DIFFRACTION98
1.8324-1.85750.27081500.21512955X-RAY DIFFRACTION96
1.8575-1.8840.24651490.20782924X-RAY DIFFRACTION97
1.884-1.91210.26211450.21232964X-RAY DIFFRACTION98
1.9121-1.9420.27631530.20792966X-RAY DIFFRACTION96
1.942-1.97380.24931520.21032979X-RAY DIFFRACTION99
1.9738-2.00790.26331490.20592931X-RAY DIFFRACTION97
2.0079-2.04440.23561640.20942963X-RAY DIFFRACTION98
2.0444-2.08370.27061680.19992945X-RAY DIFFRACTION98
2.0837-2.12620.22741790.20032949X-RAY DIFFRACTION98
2.1262-2.17250.27081490.21232985X-RAY DIFFRACTION98
2.1725-2.2230.24771500.20072991X-RAY DIFFRACTION98
2.223-2.27860.2351680.19872991X-RAY DIFFRACTION98
2.2786-2.34020.27591390.20253001X-RAY DIFFRACTION99
2.3402-2.40910.27151570.20222992X-RAY DIFFRACTION98
2.4091-2.48680.23321620.19823010X-RAY DIFFRACTION99
2.4868-2.57570.24251550.19792956X-RAY DIFFRACTION98
2.5757-2.67880.26251420.21543011X-RAY DIFFRACTION98
2.6788-2.80070.26211350.20813072X-RAY DIFFRACTION99
2.8007-2.94830.22261670.20262996X-RAY DIFFRACTION99
2.9483-3.1330.22411670.20333025X-RAY DIFFRACTION99
3.133-3.37480.2211930.18873022X-RAY DIFFRACTION99
3.3748-3.71430.21961640.18283068X-RAY DIFFRACTION100
3.7143-4.25150.1851350.18643088X-RAY DIFFRACTION99
4.2515-5.35510.20281640.17393094X-RAY DIFFRACTION99
5.3551-45.68340.2241510.21813194X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 54.0703 Å / Origin y: 63.2522 Å / Origin z: 129.9427 Å
111213212223313233
T0.038 Å20.0167 Å2-0.008 Å2-0.0504 Å2-0.0022 Å2--0.0459 Å2
L0.0024 °20.0285 °2-0.0873 °2-0.0163 °20.0056 °2--0.0461 °2
S-0.007 Å °-0.0101 Å °0.0035 Å °0.001 Å °0.0015 Å °0.0131 Å °0.0039 Å °0.0007 Å °-0.0275 Å °
Refinement TLS groupSelection details: all

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