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- PDB-6ana: LL2 Fab in complex with anti-Kappa VHH domain -

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Basic information

Entry
Database: PDB / ID: 6ana
TitleLL2 Fab in complex with anti-Kappa VHH domain
Components
  • LL2 Fab Heavy Chain
  • LL2 Fab Light Chain
  • anti Kappa VHH domain
KeywordsIMMUNE SYSTEM / Fab / antibody / CD22 / VHH domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsSicard, T. / Ereno Orbea, J. / Julien, J.-P.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments.
Authors: Ereno-Orbea, J. / Sicard, T. / Cui, H. / Carson, J. / Hermans, P. / Julien, J.P.
History
DepositionAug 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Structure summary
Category: chem_comp / database_PDB_caveat / pdbx_entry_details
Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: anti Kappa VHH domain
H: LL2 Fab Heavy Chain
L: LL2 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7954
Polymers58,2243
Non-polymers5711
Water12,376687
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-17 kcal/mol
Surface area25570 Å2
Unit cell
Length a, b, c (Å)38.925, 63.682, 68.417
Angle α, β, γ (deg.)114.28, 96.14, 91.92
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody anti Kappa VHH domain


Mass: 10400.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Antibody LL2 Fab Heavy Chain


Mass: 23701.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody LL2 Fab Light Chain


Mass: 24121.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAnti-kappa VHH domain is represented as poly-UNK. The side chains were not included in the refinement.

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 1M lithium chloride 0.1M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→38.559 Å / Num. obs: 58574 / % possible obs: 89.6 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.036 / Net I/σ(I): 15.8
Reflection shellResolution: 1.7→1.72 Å / Rmerge(I) obs: 0.362 / CC1/2: 0.765 / Rpim(I) all: 0.258

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata scaling
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHENIXphasing
RefinementResolution: 1.7→38.559 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 1991 3.4 %
Rwork0.2146 --
obs0.2154 116528 89.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 38 687 4599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044015
X-RAY DIFFRACTIONf_angle_d0.8245495
X-RAY DIFFRACTIONf_dihedral_angle_d15.2132390
X-RAY DIFFRACTIONf_chiral_restr0.047649
X-RAY DIFFRACTIONf_plane_restr0.004705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72080.3738810.30632097X-RAY DIFFRACTION47
1.7208-1.74250.3048700.29962323X-RAY DIFFRACTION52
1.7425-1.76550.3681870.28732526X-RAY DIFFRACTION54
1.7655-1.78970.30621060.28312918X-RAY DIFFRACTION65
1.7897-1.81520.30531160.26893044X-RAY DIFFRACTION70
1.8152-1.84230.3291070.25983718X-RAY DIFFRACTION81
1.8423-1.87110.23991590.26394303X-RAY DIFFRACTION95
1.8711-1.90180.28121480.24634206X-RAY DIFFRACTION96
1.9018-1.93460.30961570.2324369X-RAY DIFFRACTION95
1.9346-1.96970.27011630.22724261X-RAY DIFFRACTION96
1.9697-2.00760.2651340.22844336X-RAY DIFFRACTION96
2.0076-2.04860.22981660.22344412X-RAY DIFFRACTION96
2.0486-2.09310.26641440.21984290X-RAY DIFFRACTION97
2.0931-2.14180.26341720.21274302X-RAY DIFFRACTION96
2.1418-2.19540.28961540.20434348X-RAY DIFFRACTION97
2.1954-2.25470.25051340.2084342X-RAY DIFFRACTION96
2.2547-2.32110.23741530.20394359X-RAY DIFFRACTION97
2.3211-2.3960.24581520.20944433X-RAY DIFFRACTION97
2.396-2.48160.23761600.21474331X-RAY DIFFRACTION97
2.4816-2.5810.22121560.21674410X-RAY DIFFRACTION97
2.581-2.69840.21861620.2194307X-RAY DIFFRACTION97
2.6984-2.84060.23051540.2134402X-RAY DIFFRACTION98
2.8406-3.01850.22941540.20654403X-RAY DIFFRACTION97
3.0185-3.25150.22931560.20844426X-RAY DIFFRACTION98
3.2515-3.57850.16941500.18824411X-RAY DIFFRACTION98
3.5785-4.09580.20151560.19344409X-RAY DIFFRACTION99
4.0958-5.15830.20351540.19144460X-RAY DIFFRACTION99
5.1583-38.56940.25331560.2324421X-RAY DIFFRACTION98

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