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- PDB-3eak: NbBCII10 humanized (FGLA mutant) -

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Basic information

Entry
Database: PDB / ID: 3eak
TitleNbBCII10 humanized (FGLA mutant)
ComponentsNbBCII10-FGLA
KeywordsIMMUNE SYSTEM / antibody / nanobody / humanization / VHH domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsVincke, C. / Loris, R. / Saerens, D. / Martinez-Rodriguez, S. / Muyldermans, S. / Conrath, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold.
Authors: Vincke, C. / Loris, R. / Saerens, D. / Martinez-Rodriguez, S. / Muyldermans, S. / Conrath, K.
History
DepositionAug 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NbBCII10-FGLA
B: NbBCII10-FGLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0673
Polymers29,9712
Non-polymers961
Water3,693205
1
A: NbBCII10-FGLA


Theoretical massNumber of molelcules
Total (without water)14,9861
Polymers14,9861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NbBCII10-FGLA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0822
Polymers14,9861
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.585, 70.750, 50.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-197-

HOH

21A-198-

HOH

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Components

#1: Antibody NbBCII10-FGLA


Mass: 14985.692 Da / Num. of mol.: 2
Mutation: S11L, A14P, T23A, E47G, R48L, A78S, V82L, T83Y, N88S, K90R, P91A, I96V, Q123L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE 13 MUTATIONS S11L, A14P, T23A, E47G, R48L, A78S, V82L, T83Y, N88S, K90R, P91A, I96V, Q123L

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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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Na-Hepes pH 7.5, 2% PEG 400, 2M NH4(SO4)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.909 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 20171 / Num. obs: 20171 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.196 / Rsym value: 0.196 / Net I/σ(I): 9.99
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1998 / Rsym value: 0.607 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1zmy

1zmy


Resolution: 1.95→50 Å / Isotropic thermal model: individual isotropic B-factors / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: used mli target in cns including global anisotropic b-factor correction and bulk solvent correction
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1584 -random
Rwork0.215 ---
all-20171 --
obs-20171 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.414 Å20 Å20 Å2
2---5.764 Å20 Å2
3---4.349 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 5 205 2100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0058
X-RAY DIFFRACTIONc_angle_deg1.37

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