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- PDB-4w2p: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C -

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Basic information

Entry
Database: PDB / ID: 4w2p
TitleAnti-Marburgvirus Nucleoprotein Single Domain Antibody C
ComponentsAnti-Marburgvirus Nucleoprotein Single Domain Antibody C
KeywordsIMMUNE SYSTEM
Function / homologyACETATE ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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 1.2Sep 27, 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 C
B: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
C: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
D: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2357
Polymers56,0944
Non-polymers1413
Water6,828379
1
A: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1063
Polymers14,0241
Non-polymers822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C


Theoretical massNumber of molelcules
Total (without water)14,0241
Polymers14,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0832
Polymers14,0241
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Anti-Marburgvirus Nucleoprotein Single Domain Antibody C


Theoretical massNumber of molelcules
Total (without water)14,0241
Polymers14,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.392, 49.506, 65.406
Angle α, β, γ (deg.)87.74, 84.77, 79.41
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 14023.535 Da / Num. of mol.: 4
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 1.89 Å3/Da / Density % sol: 34.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% polyethylene glycol 550 monomethyl ether/polyethylene glycol 20000, 0.1M carboxylic acids mix (sodium formate, ammonium acetate, sodium citrate, sodium/potassium tartrate, sodium oxamate) ...Details: 30% polyethylene glycol 550 monomethyl ether/polyethylene glycol 20000, 0.1M carboxylic acids mix (sodium formate, ammonium acetate, sodium citrate, sodium/potassium tartrate, sodium oxamate), 0.1M imidazole/MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→48.65 Å / Num. obs: 36665 / % possible obs: 91.6 % / Redundancy: 2.5 % / Biso Wilson estimate: 16.3 Å2 / Rpim(I) all: 0.058 / Rsym value: 0.063 / Net I/σ(I): 8.6
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5165 / Rpim(I) all: 0.332 / Rsym value: 0.39 / % possible all: 88.5

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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: 1.77→26.772 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2031 1829 4.99 %
Rwork0.165 --
obs0.167 36633 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.77→26.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3701 0 9 379 4089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013839
X-RAY DIFFRACTIONf_angle_d1.0345195
X-RAY DIFFRACTIONf_dihedral_angle_d15.9411385
X-RAY DIFFRACTIONf_chiral_restr0.058549
X-RAY DIFFRACTIONf_plane_restr0.006680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7684-1.81620.30491330.262565X-RAY DIFFRACTION89
1.8162-1.86970.26811250.22812599X-RAY DIFFRACTION87
1.8697-1.930.21541360.18342637X-RAY DIFFRACTION92
1.93-1.99890.24831190.16882771X-RAY DIFFRACTION93
1.9989-2.0790.22371270.16752755X-RAY DIFFRACTION93
2.079-2.17350.1831350.1682715X-RAY DIFFRACTION93
2.1735-2.28810.23441490.16162643X-RAY DIFFRACTION91
2.2881-2.43130.23071640.16292525X-RAY DIFFRACTION87
2.4313-2.61890.1911320.17032822X-RAY DIFFRACTION95
2.6189-2.88220.22761720.16452706X-RAY DIFFRACTION94
2.8822-3.29860.20631380.15792688X-RAY DIFFRACTION91
3.2986-4.15340.1541380.14192687X-RAY DIFFRACTION92
4.1534-26.77540.17611610.15672691X-RAY DIFFRACTION93

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