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- PDB-5i30: Crystal structure of the human astrovirus 2 neutralizing monoclon... -

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Basic information

Entry
Database: PDB / ID: 5i30
TitleCrystal structure of the human astrovirus 2 neutralizing monoclonal antibody PL-2 Fab fragment at 1.9 A resolution
Components
  • Fab PL-2 heavy chain
  • Fab PL-2 light chain
KeywordsIMMUNE SYSTEM / antibody Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBogdanoff, W.A. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095369 United States
CitationJournal: Acs Infect Dis. / Year: 2016
Title: De Novo Sequencing and Resurrection of a Human Astrovirus-Neutralizing Antibody.
Authors: Bogdanoff, W.A. / Morgenstern, D. / Bern, M. / Ueberheide, B.M. / Sanchez-Fauquier, A. / DuBois, R.M.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq.db_align_end
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab PL-2 light chain
H: Fab PL-2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4763
Polymers47,2542
Non-polymers2211
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-20 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.220, 170.470, 78.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Fab PL-2 light chain


Mass: 23680.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab PL-2 heavy chain


Mass: 23573.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 3350, ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→38.79 Å / Num. obs: 37834 / % possible obs: 98.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.58 / Num. measured all: 34428 / Num. unique all: 5395 / CC1/2: 0.825 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Rsym value: 0.033 / Net I/σ(I) obs: 3.4 / Rejects: 0 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXPHENIX1.10-2152refinement
MOSFLM3.3.21data reduction
SCALA3.3.21data scaling
Coot0.8.2model building
PHASER6.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NCA

1nca


Resolution: 1.9→38.788 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.27
RfactorNum. reflection% reflection
Rfree0.2212 1904 5.03 %
Rwork0.1796 --
obs0.1818 37831 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.32 Å2 / Biso mean: 23.952 Å2 / Biso min: 7.82 Å2
Refinement stepCycle: final / Resolution: 1.9→38.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 14 115 3378
Biso mean--73.18 24.26 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133402
X-RAY DIFFRACTIONf_angle_d1.3364652
X-RAY DIFFRACTIONf_chiral_restr0.079528
X-RAY DIFFRACTIONf_plane_restr0.009592
X-RAY DIFFRACTIONf_dihedral_angle_d13.8932038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94750.2531300.22182479260997
1.9475-2.00020.2261380.192504264297
2.0002-2.0590.20731420.18252529267197
2.059-2.12550.24771110.17682541265298
2.1255-2.20140.21491300.16582533266398
2.2014-2.28960.2091450.17532512265798
2.2896-2.39380.19861330.17882555268899
2.3938-2.51990.23641210.1772578269999
2.5199-2.67780.24381350.18732577271299
2.6778-2.88450.22661420.19482587272999
2.8845-3.17460.25561420.18832562270499
3.1746-3.63370.21841140.1812641275599
3.6337-4.57690.20111590.16452589274899
4.5769-38.79620.21621620.17432740290299
Refinement TLS params.Method: refined / Origin x: -16.8519 Å / Origin y: -25.9887 Å / Origin z: -10.3584 Å
111213212223313233
T0.1404 Å2-0.0238 Å20.0113 Å2-0.1194 Å20.0101 Å2--0.1624 Å2
L0.5321 °2-0.046 °2-0.4053 °2-0.1493 °2-0.1227 °2--0.8791 °2
S0.1058 Å °0.0026 Å °0.1814 Å °-0.0034 Å °-0.0313 Å °0.0294 Å °-0.2403 Å °0.0217 Å °-0.0339 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1
2X-RAY DIFFRACTION1allL1 - 212
3X-RAY DIFFRACTION1allH1 - 222
4X-RAY DIFFRACTION1allA1 - 323

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