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- PDB-4h20: Crystal Structure and Computational Modeling of the Fab Fragment ... -

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Basic information

Entry
Database: PDB / ID: 4h20
TitleCrystal Structure and Computational Modeling of the Fab Fragment from the Protective anti-Ricin Monoclonal Antibody RAC18
Components
  • Heavy chain of Fab Fragment from the anti-Ricin Monoclonal Antibody RAC18
  • Light chain of Fab Fragment from the anti-Ricin Monoclonal Antibody RAC18
KeywordsIMMUNE SYSTEM / Ig / Anti Ricin Antibody Fab fragment / Ricin A chain / extracellular / bloodstream
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhao, Z. / Worthylake, D.K. / LeCour Jr., L.F. / Maresh, G. / Pincus, S.H.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure and computational modeling of the fab fragment from a protective anti-ricin monoclonal antibody.
Authors: Zhao, Z. / Worthylake, D. / Lecour, L. / Maresh, G.A. / Pincus, S.H.
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of Fab Fragment from the anti-Ricin Monoclonal Antibody RAC18
H: Heavy chain of Fab Fragment from the anti-Ricin Monoclonal Antibody RAC18


Theoretical massNumber of molelcules
Total (without water)47,0582
Polymers47,0582
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.640, 85.930, 130.070
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 Light chain of Fab Fragment from the anti-Ricin Monoclonal Antibody RAC18


Mass: 23630.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Heavy chain of Fab Fragment from the anti-Ricin Monoclonal Antibody RAC18


Mass: 23427.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.4
Details: 25 mM NaCl, 10 mM Tris-HCl (pH 7.4),1 mM EDTA, 95-98 mM lithium nitrate, 20% w/v PEG 3350, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 19, 2011 / Details: Helios
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→14.8 Å / Num. all: 34728 / Num. obs: 34728 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 5.6 Å2 / Rsym value: 4.28 / Net I/σ(I): 22.67
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 7.68 / Num. unique all: 4383 / Rsym value: 9.34 / % possible all: 87

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNS1.1refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3DIF chain A, PDB ID 1EGJ chain H

3dif

1egj


Resolution: 1.9→14.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2070 -RANDOM
Rwork0.195 ---
all0.197 34728 --
obs0.197 34728 96.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 382 3689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBond Lengths0.005
X-RAY DIFFRACTIONBond Angles1.4
X-RAY DIFFRACTIONDihedral Angles27.1
X-RAY DIFFRACTIONImproper Angles0.75
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.239 318 -
Rwork0.202 --
obs-4880 88.8 %

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