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- PDB-2a6k: Crystal Structure Analysis of the germline antibody 36-65 Fab in ... -

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Basic information

Entry
Database: PDB / ID: 2a6k
TitleCrystal Structure Analysis of the germline antibody 36-65 Fab in complex with the dodecapeptide SLGDNLTNHNLR
Components
  • DODECAPEPTIDE: SLGDNLTNHNLR
  • Germline antibody 36-65 Fab heavy chain
  • Germline antibody 36-65 Fab light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Fab-peptide complex
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 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 3, 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 21, 2018Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
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

Downloads & links

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Assembly

Deposited unit
A: Germline antibody 36-65 Fab light chain
B: Germline antibody 36-65 Fab heavy chain
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab heavy chain
P: DODECAPEPTIDE: SLGDNLTNHNLR


Theoretical massNumber of molelcules
Total (without water)96,6555
Polymers96,6555
Non-polymers00
Water1,856103
1
A: Germline antibody 36-65 Fab light chain
B: 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 area3770 Å2
ΔGint-25 kcal/mol
Surface area19760 Å2
MethodPISA
2
L: Germline antibody 36-65 Fab light chain
H: Germline antibody 36-65 Fab heavy chain
P: DODECAPEPTIDE: SLGDNLTNHNLR


Theoretical massNumber of molelcules
Total (without water)49,0053
Polymers49,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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 area3630 Å2
ΔGint-26 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.135, 144.920, 70.991
Angle α, β, γ (deg.)90.00, 104.35, 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)
#2: Antibody Germline antibody 36-65 Fab heavy chain


Mass: 23942.768 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: mouse monoclonal / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6PF95
#3: Protein/peptide DODECAPEPTIDE: SLGDNLTNHNLR


Mass: 1355.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized peptide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.6 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 20% PEG 8000, cacodylate, 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: Aug 10, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 19662 / Num. obs: 19662 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.04 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 4
Reflection shellResolution: 3→3.11 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
MAR345data collection
AUTOMARdata reduction
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1813 8.7 %random
Rwork0.245 ---
all0.246 20866 --
obs0.246 18490 88.6 %-
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6661 0 0 103 6764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.73493
X-RAY DIFFRACTIONc_bond_d0.01013

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