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- PDB-6apq: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B -

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Basic information

Entry
Database: PDB / ID: 6apq
TitleAnti-Marburgvirus Nucleoprotein Single Domain Antibody B
ComponentsAnti-Marburgvirus Nucleoprotein Single Domain Antibody B
KeywordsIMMUNE SYSTEM
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTaylor, A.B. / Garza, J.A.
CitationJournal: Front Immunol / Year: 2017
Title: Unveiling a Drift Resistant Cryptotope withinMarburgvirusNucleoprotein Recognized by Llama Single-Domain Antibodies.
Authors: Garza, J.A. / Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-Marburgvirus Nucleoprotein Single Domain Antibody B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8885
Polymers13,7581
Non-polymers1294
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.988, 79.988, 89.894
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-427-

HOH

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Components

#1: Antibody Anti-Marburgvirus Nucleoprotein Single Domain Antibody B


Mass: 13758.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Description: Semi-synthetic single pot library Nomad 1 based upon Lama glama
Plasmid: pecan73 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 4.0M sodium chloride, 0.1M bicine pH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.9→69.27 Å / Num. obs: 13942 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.9 Å2 / Rpim(I) all: 0.043 / Rsym value: 0.084 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1987 / Rpim(I) all: 0.304 / Rsym value: 0.587 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6APO

6apo


Resolution: 1.9→69.27 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.98
RfactorNum. reflection% reflection
Rfree0.2167 1390 10 %
Rwork0.1847 --
obs0.1879 13899 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 4 135 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007922
X-RAY DIFFRACTIONf_angle_d1.1031243
X-RAY DIFFRACTIONf_dihedral_angle_d18.824333
X-RAY DIFFRACTIONf_chiral_restr0.053129
X-RAY DIFFRACTIONf_plane_restr0.004161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.28561350.24651216X-RAY DIFFRACTION100
1.9679-2.04670.26911350.22751215X-RAY DIFFRACTION100
2.0467-2.13990.25381360.20361220X-RAY DIFFRACTION100
2.1399-2.25270.23811370.18061230X-RAY DIFFRACTION100
2.2527-2.39390.28271370.20671236X-RAY DIFFRACTION100
2.3939-2.57870.2451370.20361243X-RAY DIFFRACTION100
2.5787-2.83820.24121380.18941241X-RAY DIFFRACTION100
2.8382-3.24890.21741390.18781258X-RAY DIFFRACTION100
3.2489-4.09320.16461440.15791286X-RAY DIFFRACTION100
4.0932-69.31770.19621520.17411364X-RAY DIFFRACTION99

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