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- PDB-2a6d: Crystal structure analysis of the anti-arsonate germline antibody... -

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Basic information

Entry
Database: PDB / ID: 2a6d
TitleCrystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE
Components
  • Dodecapeptide, RLLIADPPSPRE
  • Germline antibody 36-65 Fab Heavy chain
  • Germline antibody 36-65 Fab light chain
KeywordsIMMUNE SYSTEM / Germline / FAB / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M.
CitationJournal: Immunity / Year: 2006
Title: Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response.
Authors: Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M.
History
DepositionJul 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.4Aug 23, 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
Remark 999SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS ...SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS B,H WHICH CORRESPOND TO DEPOSITED SEQUENCE OF THE HEAVY CHAIN VARIABLE REGION OF ANTI-ARSONATE ANTIBODY 36-65

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab Heavy chain
A: Germline antibody 36-65 Fab light chain
B: Germline antibody 36-65 Fab Heavy chain
P: Dodecapeptide, RLLIADPPSPRE


Theoretical massNumber of molelcules
Total (without water)96,6655
Polymers96,6655
Non-polymers00
Water1,40578
1
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6502
Polymers47,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-27 kcal/mol
Surface area19820 Å2
MethodPISA
2
A: Germline antibody 36-65 Fab light chain
B: Germline antibody 36-65 Fab Heavy chain
P: Dodecapeptide, RLLIADPPSPRE


Theoretical massNumber of molelcules
Total (without water)49,0153
Polymers49,0153
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.302, 145.670, 71.347
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Germline antibody 36-65 Fab light chain


Mass: 23707.049 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse) / Strain: A/J
#2: Antibody Germline antibody 36-65 Fab Heavy chain


Mass: 23942.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Dodecapeptide, RLLIADPPSPRE


Mass: 1365.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized (Phage display derived peptide)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.7 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 18% PEG 8000, cacodylate, 0.05% azide, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 23421 / Num. obs: 23421 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.87

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAB

6fab


Resolution: 2.9→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1787 -RANDOM
Rwork0.23 ---
all0.232 23395 --
obs0.232 18109 77.4 %-
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 0 78 6792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.83949
X-RAY DIFFRACTIONc_bond_d0.012067

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