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- PDB-3eo9: Crystal structure the Fab fragment of Efalizumab -

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Basic information

Entry
Database: PDB / ID: 3eo9
TitleCrystal structure the Fab fragment of Efalizumab
Components
  • Efalizumab Fab fragment, heavy chain
  • Efalizumab Fab fragment, light chain
KeywordsIMMUNE SYSTEM / Efalizumab / Fab / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, S. / Ding, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Efalizumab binding to the LFA-1 alphaL I domain blocks ICAM-1 binding via steric hindrance.
Authors: Li, S. / Wang, H. / Peng, B. / Zhang, M. / Zhang, D. / Hou, S. / Guo, Y. / Ding, J.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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: Efalizumab Fab fragment, light chain
H: Efalizumab Fab fragment, heavy chain


Theoretical massNumber of molelcules
Total (without water)47,0592
Polymers47,0592
Non-polymers00
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-26 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.198, 87.198, 117.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Efalizumab Fab fragment, light chain


Mass: 23436.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1
#2: Antibody Efalizumab Fab fragment, heavy chain


Mass: 23622.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGG1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15mM citric acid, 12% w/v PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 2, 2007 / Details: Confocal
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 48198 / Num. obs: 47282 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4699 / Rsym value: 0.373 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
REFMAC5.1.24refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B2W

1b2w


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.213 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21702 2347 5 %RANDOM
Rwork0.18932 ---
all0.1907 45884 --
obs0.1907 44966 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.482 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 0 625 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213287
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9434455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955416
X-RAY DIFFRACTIONr_chiral_restr0.0810.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022449
X-RAY DIFFRACTIONr_gen_planes_other00.021
X-RAY DIFFRACTIONr_nbd_refined0.2230.21500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2543
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.249
X-RAY DIFFRACTIONr_mcbond_it0.6641.52105
X-RAY DIFFRACTIONr_mcangle_it1.15123387
X-RAY DIFFRACTIONr_scbond_it2.37831182
X-RAY DIFFRACTIONr_scangle_it2.484.51067
X-RAY DIFFRACTIONr_rigid_bond_restr2.55823287
X-RAY DIFFRACTIONr_sphericity_free2.1412637
X-RAY DIFFRACTIONr_sphericity_bonded1.1323213
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 179
Rwork0.266 3295

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