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- PDB-3sgd: Crystal structure of the mouse mAb 17.2 -

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Basic information

Entry
Database: PDB / ID: 3sgd
TitleCrystal structure of the mouse mAb 17.2
Components
  • Heavy Chain
  • Light Chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / Antibody / Antigen binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsPizarro, J.C. / Boulot, G. / Hontebeyrie, M. / Bentley, G.A.
CitationJournal: Plos Negl Trop Dis / Year: 2011
Title: Crystal structure of the complex mAb 17.2 and the C-terminal region of Trypanosoma cruzi P2 Beta protein: implications in cross-reactivity
Authors: Pizarro, J.C. / Boulot, G. / Bentley, G.A. / Gomez, K.A. / Hoebeke, J. / Hontebeyrie, M. / Levin, M.J. / Smulski, C.R.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light Chain
H: Heavy Chain
I: Light Chain
J: Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5497
Polymers95,4294
Non-polymers1203
Water10,755597
1
L: Light Chain
H: Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7954
Polymers47,7142
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-41 kcal/mol
Surface area20020 Å2
MethodPISA
2
I: Light Chain
J: Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7543
Polymers47,7142
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-28 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.760, 65.460, 91.030
Angle α, β, γ (deg.)90.00, 98.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light Chain


Mass: 24178.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Cell: HYBRIDOMA
#2: Antibody Heavy Chain


Mass: 23535.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Cell: HYBRIDOMA
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 597 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 18% PEG 8000, 0.1M sodium cacodylate pH 6.7, 0.2M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 122 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.89→30 Å / Num. obs: 41489 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.82 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.9.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→18.93 Å / Cor.coef. Fo:Fc: 0.9495 / Cor.coef. Fo:Fc free: 0.9112 / SU R Cruickshank DPI: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 2082 5.02 %RANDOM
Rwork0.1724 ---
all0.1756 ---
obs0.1756 41489 98.84 %-
Displacement parametersBiso mean: 33.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.2304 Å20 Å22.1491 Å2
2---0.4326 Å20 Å2
3----0.7978 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.31→18.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6663 0 3 597 7263
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016871HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.259366HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2311SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes153HARMONIC2
X-RAY DIFFRACTIONt_gen_planes999HARMONIC5
X-RAY DIFFRACTIONt_it6871HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion19.66
X-RAY DIFFRACTIONt_chiral_improper_torsion925SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8275SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3122 111 4.12 %
Rwork0.2013 2581 -
all0.2057 2692 -
obs--98.84 %

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