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- PDB-3ojd: Anti-Indolicidin monoclonal antibody V2D2 (Fab fragment) -

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Basic information

Entry
Database: PDB / ID: 3ojd
TitleAnti-Indolicidin monoclonal antibody V2D2 (Fab fragment)
Components(Fab V2D2) x 2
KeywordsIMMUNE SYSTEM / Beta-sandwich Immunoglobulin fold / Antigen binding / Secreted protein / anti-indolicidin Fab / surrogate receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLomash, S. / Salunke, D.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: An antibody as surrogate receptor reveals determinants of activity of an innate immune peptide antibiotic
Authors: Lomash, S. / Nagpal, S. / Salunke, D.M.
History
DepositionAug 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab V2D2
B: Fab V2D2


Theoretical massNumber of molelcules
Total (without water)47,8142
Polymers47,8142
Non-polymers00
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-23 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.190, 63.71, 164.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab V2D2


Mass: 23415.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Light chain / Source: (natural) Mus musculus (house mouse) / Cell: B-cells / Organ: Spleen / Strain: BALB/c
#2: Antibody Fab V2D2


Mass: 24398.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Heavy chain / Source: (natural) Mus musculus (house mouse) / Cell: B-cells / Organ: Spleen / Strain: BALB/c
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 10% PEG 1000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 21, 2006 / Details: mirrors
RadiationMonochromator: Ni FILTER CMF12 38Cu-6 (Osmic Inc.) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 31660 / Num. obs: 28494 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Redundancy: 5.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.5
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3 / % possible all: 75.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
CNS1.3refinement
AUTOMARdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YMH

1ymh


Resolution: 2→41.5 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 2856 RANDOM
Rwork0.205 --
all0.206 28434 -
obs-25578 -
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 0 388 3741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.295 689 -
Rwork0.262 --
obs-6612 77.8 %

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