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- PDB-6apo: Anti-Marburgvirus Nucleoprotein Single Domain Antibody A -

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Basic information

Entry
Database: PDB / ID: 6apo
TitleAnti-Marburgvirus Nucleoprotein Single Domain Antibody A
ComponentsAnti-Marburgvirus Nucleoprotein Single Domain Antibody A
KeywordsIMMUNE SYSTEM / single domain antibody
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.168 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-Marburgvirus Nucleoprotein Single Domain Antibody A


Theoretical massNumber of molelcules
Total (without water)14,2161
Polymers14,2161
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.597, 49.362, 58.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14215.889 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25% polyethylene glycol 1000, 0.1M Tris-HCl pH 8.5

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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 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.168→41.6 Å / Num. obs: 40045 / % possible obs: 95.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 9.3 Å2 / Rpim(I) all: 0.028 / Rsym value: 0.067 / Net I/σ(I): 17.6
Reflection shellResolution: 1.17→1.23 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4261 / Rpim(I) all: 0.198 / Rsym value: 0.282 / % possible all: 71.3

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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: 1YC7

1yc7


Resolution: 1.168→37.81 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.94
RfactorNum. reflection% reflection
Rfree0.1728 2000 5 %
Rwork0.1477 --
obs0.149 39980 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 1.168→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 0 176 1094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007980
X-RAY DIFFRACTIONf_angle_d0.9671341
X-RAY DIFFRACTIONf_dihedral_angle_d13.887369
X-RAY DIFFRACTIONf_chiral_restr0.086145
X-RAY DIFFRACTIONf_plane_restr0.008173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.168-1.19710.219800.17771506X-RAY DIFFRACTION54
1.1971-1.22940.18561260.15862415X-RAY DIFFRACTION87
1.2294-1.26560.16671480.13712798X-RAY DIFFRACTION100
1.2656-1.30650.1551460.12652786X-RAY DIFFRACTION100
1.3065-1.35320.13891460.12492775X-RAY DIFFRACTION100
1.3532-1.40730.14951490.12212822X-RAY DIFFRACTION100
1.4073-1.47140.14231480.11992815X-RAY DIFFRACTION100
1.4714-1.5490.14351480.1232811X-RAY DIFFRACTION100
1.549-1.6460.13641490.12562826X-RAY DIFFRACTION100
1.646-1.77310.18231490.1362829X-RAY DIFFRACTION100
1.7731-1.95150.15121500.14012847X-RAY DIFFRACTION100
1.9515-2.23390.16691510.14772860X-RAY DIFFRACTION100
2.2339-2.81430.18441520.17242898X-RAY DIFFRACTION100
2.8143-37.810.20181580.16212992X-RAY DIFFRACTION99

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