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- PDB-6btj: Crystal structure of pan-H7, anti-hemagglutinin monoclonal antibo... -

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Basic information

Entry
Database: PDB / ID: 6btj
TitleCrystal structure of pan-H7, anti-hemagglutinin monoclonal antibody H7.5 (Fab fragment)
Components
  • Heavy chain of H7.5 Fab
  • Light chain of H7.5 Fab
KeywordsANTIVIRAL PROTEIN / anti-HA neutralizing antibody / H7 specific
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.999 Å
AuthorsShanshan, L. / Ian, A.W.
CitationJournal: To Be Published
Title: Crystal structure of pan-H7, anti-hemagglutinin monoclonal antibody H7.5 (Fab fragment)
Authors: Andrew, B.W. / Ian, A.W. / James, E.C. / Hannah, T. / Shanshan, L. / Jesper, P. / Sandhya, B.
History
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of H7.5 Fab
B: Light chain of H7.5 Fab
H: Heavy chain of H7.5 Fab
L: Light chain of H7.5 Fab


Theoretical massNumber of molelcules
Total (without water)97,1044
Polymers97,1044
Non-polymers00
Water13,421745
1
A: Heavy chain of H7.5 Fab
B: Light chain of H7.5 Fab


Theoretical massNumber of molelcules
Total (without water)48,5522
Polymers48,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area19370 Å2
MethodPISA
2
H: Heavy chain of H7.5 Fab
L: Light chain of H7.5 Fab


Theoretical massNumber of molelcules
Total (without water)48,5522
Polymers48,5522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-26 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.510, 99.038, 208.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-317-

HOH

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Components

#1: Antibody Heavy chain of H7.5 Fab


Mass: 25108.170 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 H7.5 Fab


Mass: 23443.979 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.: 745 / 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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH6.5 0.01M cobalt chloride 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 91327 / % possible obs: 98.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 31 Å2 / CC1/2: 1 / Rpim(I) all: 0.047 / Rrim(I) all: 0.123 / Net I/av σ(I): 21 / Net I/σ(I): 21
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4421 / CC1/2: 0.79 / Rpim(I) all: 0.32 / Rrim(I) all: 0.81 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
SCALAdata scaling
PARROTphasing
RefinementResolution: 1.999→49.519 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 4560 5 %
Rwork0.1997 --
obs0.1998 91238 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→49.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 0 745 7300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096742
X-RAY DIFFRACTIONf_angle_d1.1389172
X-RAY DIFFRACTIONf_dihedral_angle_d18.182442
X-RAY DIFFRACTIONf_chiral_restr0.0661028
X-RAY DIFFRACTIONf_plane_restr0.0071170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.02170.31671240.27862795X-RAY DIFFRACTION96
2.0217-2.04550.30071650.27632820X-RAY DIFFRACTION97
2.0455-2.07050.32671470.27592777X-RAY DIFFRACTION97
2.0705-2.09670.29321560.26332797X-RAY DIFFRACTION97
2.0967-2.12430.25811610.24572863X-RAY DIFFRACTION98
2.1243-2.15340.2711480.23412801X-RAY DIFFRACTION97
2.1534-2.18410.22861480.22922854X-RAY DIFFRACTION98
2.1841-2.21670.25531420.23162822X-RAY DIFFRACTION98
2.2167-2.25140.28711490.26882883X-RAY DIFFRACTION98
2.2514-2.28830.25751700.25142809X-RAY DIFFRACTION98
2.2883-2.32770.25031380.22122886X-RAY DIFFRACTION98
2.3277-2.37010.22741520.22342861X-RAY DIFFRACTION98
2.3701-2.41560.25541410.22942893X-RAY DIFFRACTION99
2.4156-2.46490.22541430.22132834X-RAY DIFFRACTION99
2.4649-2.51850.2421590.22492901X-RAY DIFFRACTION99
2.5185-2.57710.22051730.21782849X-RAY DIFFRACTION99
2.5771-2.64160.23171510.21392878X-RAY DIFFRACTION99
2.6416-2.7130.21021480.21692895X-RAY DIFFRACTION99
2.713-2.79280.22461570.22132887X-RAY DIFFRACTION99
2.7928-2.88290.24381460.21472895X-RAY DIFFRACTION99
2.8829-2.9860.22021520.20582920X-RAY DIFFRACTION99
2.986-3.10550.19371470.20552902X-RAY DIFFRACTION99
3.1055-3.24680.19781520.19572906X-RAY DIFFRACTION99
3.2468-3.4180.19041470.19542954X-RAY DIFFRACTION99
3.418-3.6320.19151500.18362921X-RAY DIFFRACTION99
3.632-3.91240.17031620.17922938X-RAY DIFFRACTION99
3.9124-4.30590.13921560.1512977X-RAY DIFFRACTION99
4.3059-4.92850.1211520.14142989X-RAY DIFFRACTION100
4.9285-6.20740.18491630.17933021X-RAY DIFFRACTION99
6.2074-49.53420.19461610.21043150X-RAY DIFFRACTION99

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