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- PDB-3eo0: Structure of the Transforming Growth Factor-Beta Neutralizing Ant... -

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Basic information

Entry
Database: PDB / ID: 3eo0
TitleStructure of the Transforming Growth Factor-Beta Neutralizing Antibody GC-1008
Components
  • GC-1008 Fab Heavy Chain
  • GC-1008 Fab Light Chain
KeywordsIMMUNE SYSTEM / Cytokine neutralizing antibody / FAB fragment
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
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/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
Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsGruetter, C. / Gruetter, M.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions
Authors: Wilkinson, T. / Turner, R. / Podichetty, S. / Finch, D. / McCourt, M. / Loning, S. / Jermutus, L.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GC-1008 Fab Light Chain
B: GC-1008 Fab Heavy Chain
C: GC-1008 Fab Light Chain
D: GC-1008 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,10210
Polymers94,5504
Non-polymers5536
Water13,818767
1
A: GC-1008 Fab Light Chain
B: GC-1008 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5515
Polymers47,2752
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-30.4 kcal/mol
Surface area19460 Å2
MethodPISA
2
C: GC-1008 Fab Light Chain
D: GC-1008 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5515
Polymers47,2752
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-30 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.561, 83.009, 91.824
Angle α, β, γ (deg.)90.000, 103.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody GC-1008 Fab Light Chain


Mass: 23425.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / Strain (production host): NS0
#2: Antibody GC-1008 Fab Heavy Chain


Mass: 23848.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / Strain (production host): NS0 / References: UniProt: Q6PYX1*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.59 Å3/Da / Density % sol: 65.74 % / Mosaicity: 0.674 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG4000, 0.1M MOPS, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9764 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 19, 2006 / Details: BENT MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 130926 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.074 / Χ2: 1 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.812.50.306114740.993185.8
1.81-1.892.90.26129211.003197
1.89-1.973.10.2133451.074199.7
1.97-2.073.20.148133361.14199.8
2.07-2.23.20.114133761.088199.7
2.2-2.383.20.097133311.081199.6
2.38-2.613.20.077133401.032199.6
2.61-2.993.20.067133450.972199.3
2.99-3.773.10.06133810.887199.2
3.77-5030.059130770.685195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7N

2v7n


Resolution: 1.75→35.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.87 / SU B: 3.998 / SU ML: 0.058 / SU R Cruickshank DPI: 0.11 / SU Rfree: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1286 1 %RANDOM
Rwork0.182 ---
obs0.183 130868 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.81 Å2 / Biso mean: 25.544 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-1.06 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 36 767 7367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226845
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9679368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3515926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80624.263251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.371151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0371530
X-RAY DIFFRACTIONr_chiral_restr0.1120.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025152
X-RAY DIFFRACTIONr_nbd_refined0.2010.22980
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2658
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.252
X-RAY DIFFRACTIONr_mcbond_it1.4141.54531
X-RAY DIFFRACTIONr_mcangle_it2.17427191
X-RAY DIFFRACTIONr_scbond_it2.91432654
X-RAY DIFFRACTIONr_scangle_it4.1224.52147
X-RAY DIFFRACTIONr_rigid_bond_restr1.98437185
X-RAY DIFFRACTIONr_sphericity_free6.8993770
X-RAY DIFFRACTIONr_sphericity_bonded5.68536667
LS refinement shellResolution: 1.751→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 73 -
Rwork0.201 7953 -
all-8026 -
obs--100 %

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