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- PDB-3uls: Crystal structure of Fab12 -

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Basic information

Entry
Database: PDB / ID: 3uls
TitleCrystal structure of Fab12
Components
  • Fab12 heavy chain
  • Fab12 light chain
KeywordsIMMUNE SYSTEM / Toll-like receptor-3 / TLR3 / innate immunity / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.495 Å
AuthorsLuo, J. / Gilliland, G.L. / Obmolova, O. / Malia, T. / Teplyakov, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Lateral Clustering of TLR3:dsRNA Signaling Units Revealed by TLR3ecd:3Fabs Quaternary Structure.
Authors: Luo, J. / Obmolova, G. / Malia, T.J. / Wu, S.J. / Duffy, K.E. / Marion, J.D. / Bell, J.K. / Ge, P. / Zhou, Z.H. / Teplyakov, A. / Zhao, Y. / Lamb, R.J. / Jordan, J.L. / San Mateo, L.R. / ...Authors: Luo, J. / Obmolova, G. / Malia, T.J. / Wu, S.J. / Duffy, K.E. / Marion, J.D. / Bell, J.K. / Ge, P. / Zhou, Z.H. / Teplyakov, A. / Zhao, Y. / Lamb, R.J. / Jordan, J.L. / San Mateo, L.R. / Sweet, R.W. / Gilliland, G.L.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 2.0Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 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: Fab12 light chain
H: Fab12 heavy chain
A: Fab12 light chain
B: Fab12 heavy chain


Theoretical massNumber of molelcules
Total (without water)94,6174
Polymers94,6174
Non-polymers00
Water6,305350
1
L: Fab12 light chain
H: Fab12 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3082
Polymers47,3082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-29 kcal/mol
Surface area20130 Å2
MethodPISA
2
A: Fab12 light chain
B: Fab12 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3082
Polymers47,3082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-30 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.800, 80.210, 83.050
Angle α, β, γ (deg.)90.00, 115.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab12 light chain


Mass: 22732.877 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Fab12 heavy chain


Mass: 24575.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 18% PEG8000, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 10, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.495→34.4 Å / Num. all: 30263 / Num. obs: 30263 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.5
Reflection shellResolution: 2.495→2.56 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 79.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G6D

3g6d


Resolution: 2.495→34.397 Å / SU ML: 0.72 / σ(F): 1.99 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 1999 6.61 %RANDOM
Rwork0.2116 ---
obs0.2152 30247 96.3 %-
all-30247 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.797 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3709 Å20 Å216.4694 Å2
2--0.9441 Å2-0 Å2
3----0.5731 Å2
Refinement stepCycle: LAST / Resolution: 2.495→34.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6572 0 0 350 6922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036751
X-RAY DIFFRACTIONf_angle_d0.7199221
X-RAY DIFFRACTIONf_dihedral_angle_d10.0512389
X-RAY DIFFRACTIONf_chiral_restr0.0461041
X-RAY DIFFRACTIONf_plane_restr0.0041185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.495-2.55690.37221160.2771617X-RAY DIFFRACTION79
2.5569-2.6260.35561480.28022006X-RAY DIFFRACTION96
2.626-2.70320.37061380.2832017X-RAY DIFFRACTION96
2.7032-2.79050.37561270.27072019X-RAY DIFFRACTION97
2.7905-2.89010.34871520.2642011X-RAY DIFFRACTION97
2.8901-3.00580.32981460.24762024X-RAY DIFFRACTION97
3.0058-3.14250.31871430.24022055X-RAY DIFFRACTION98
3.1425-3.30810.2791490.22762058X-RAY DIFFRACTION98
3.3081-3.51510.26521410.22632025X-RAY DIFFRACTION98
3.5151-3.78620.25311550.21322094X-RAY DIFFRACTION99
3.7862-4.16670.24871440.19682035X-RAY DIFFRACTION98
4.1667-4.76820.22691410.16372054X-RAY DIFFRACTION97
4.7682-6.00230.2161450.17582089X-RAY DIFFRACTION99
6.0023-34.40010.19431540.17322144X-RAY DIFFRACTION99

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