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- PDB-1qd0: CAMELID HEAVY CHAIN VARIABLE DOMAINS PROVIDE EFFICIENT COMBINING ... -

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Basic information

Entry
Database: PDB / ID: 1qd0
TitleCAMELID HEAVY CHAIN VARIABLE DOMAINS PROVIDE EFFICIENT COMBINING SITES TO HAPTENS
ComponentsVHH-R2 ANTI-RR6 ANTIBODY
KeywordsIMMUNE SYSTEM / CAMELID VH / IMMUNOGLOBULIN FRAGMENT / AZO-DYE
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / metal ion binding
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Chem-RR6 / : / R2 protein
Similarity search - Component
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSpinelli, S. / Frenken, L.G.J. / Hermans, P. / Verrips, T. / Brown, K. / Tegoni, M. / Cambillau, C.
Citation
Journal: Biochemistry / Year: 2000
Title: Camelid heavy-chain variable domains provide efficient combining sites to haptens.
Authors: Spinelli, S. / Frenken, L.G. / Hermans, P. / Verrips, T. / Brown, K. / Tegoni, M. / Cambillau, C.
#1: Journal: Nature / Year: 1993
Title: Naturally Occurring Antibodies Devoid of Light Chains
Authors: Hamers-Casterman, C. / Atarhouch, T. / Muyldermans, S. / Robinson, G. / Hamers, C. / Songa, E.B. / Bendahman, N. / Hamers, R.
History
DepositionJul 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: VHH-R2 ANTI-RR6 ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1714
Polymers13,9281
Non-polymers1,2433
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VHH-R2 ANTI-RR6 ANTIBODY
hetero molecules

A: VHH-R2 ANTI-RR6 ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3418
Polymers27,8552
Non-polymers2,4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3520 Å2
ΔGint-90 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 46.700, 121.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody VHH-R2 ANTI-RR6 ANTIBODY


Mass: 13927.599 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN OF A HEAVY CHAIN ANTIBODY / Source method: isolated from a natural source / Source: (natural) Lama glama (llama) / Cell: PERIPHERAL BLOOD LYMPHOCYTE / Tissue: BLOOD / References: GenBank: 4165532, UniProt: A2KD59*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-RR6 / 3-HYDROXY-7-(4-{1-[2-HYDROXY-3-(2-HYDROXY-5-SULFO-PHENYLAZO)-BENZYL]-2-SULFO-ETHYLAMINO}-[1,2,5]TRIAZIN-2-YLAMINO)-2-(2-HYDROXY-5-SULFO-PHENYLAZO)-NAPTHALENE-1,8-DISULFONIC ACID / AZO-DYE RR6 HAPTEN


Mass: 1116.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H25N9O22S6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: ammonium sulfate, sodium acetate, glycerol, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMhapten1drop
211 mg/mlVHH 1drop
310 mMTris-HCl1drop
41.3 Mammonium sulfate1reservoir
5100 mMsodium acetate1reservoir
66-7 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: OTHER / Detector: CCD / Date: Apr 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 57351 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.25 / % possible all: 62
Reflection
*PLUS
Num. obs: 8364 / Num. measured all: 57351
Reflection shell
*PLUS
% possible obs: 62 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
AUTOMARdata reduction
AMoREphasing
X-PLOR3.843refinement
RefinementResolution: 2.5→12 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 800 -RANDOM
Rwork0.21 ---
obs0.21 8300 80 %-
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 74 54 1105
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 8157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_deg1.03

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