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- PDB-4j1u: Crystal structure of antibody 93F3 unstable variant -

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Basic information

Entry
Database: PDB / ID: 4j1u
TitleCrystal structure of antibody 93F3 unstable variant
Components
  • antibody 93F3 Heavy chain
  • antibody 93F3 Light chain
KeywordsIMMUNE SYSTEM / antibody maturation / antibody stability / clonal selection
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsWang, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Somatic hypermutation maintains antibody thermodynamic stability during affinity maturation.
Authors: Wang, F. / Sen, S. / Zhang, Y. / Ahmad, I. / Zhu, X. / Wilson, I.A. / Smider, V.V. / Magliery, T.J. / Schultz, P.G.
History
DepositionFeb 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody 93F3 Light chain
B: antibody 93F3 Heavy chain
C: antibody 93F3 Light chain
D: antibody 93F3 Heavy chain
E: antibody 93F3 Light chain
F: antibody 93F3 Heavy chain


Theoretical massNumber of molelcules
Total (without water)148,0296
Polymers148,0296
Non-polymers00
Water1,40578
1
A: antibody 93F3 Light chain
B: antibody 93F3 Heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3432
Polymers49,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-18 kcal/mol
Surface area18730 Å2
MethodPISA
2
C: antibody 93F3 Light chain
D: antibody 93F3 Heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3432
Polymers49,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-20 kcal/mol
Surface area19060 Å2
MethodPISA
3
E: antibody 93F3 Light chain
F: antibody 93F3 Heavy chain


Theoretical massNumber of molelcules
Total (without water)49,3432
Polymers49,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-17 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.031, 112.571, 86.509
Angle α, β, γ (deg.)90.00, 115.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody antibody 93F3 Light chain


Mass: 23988.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody antibody 93F3 Heavy chain


Mass: 25354.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 48.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris, 18% PEG6000, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 41988 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.094 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1 / Rsym value: 0.589 / % possible all: 81.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→78.33 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.904 / SU B: 33.771 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.386 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27564 2121 5.1 %RANDOM
Rwork0.20973 ---
obs0.21306 39844 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.975 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0 Å2-3.71 Å2
2---1.96 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.58→78.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9492 0 0 78 9570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.029714
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9613210
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98751249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42824.942344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.717151586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2061523
X-RAY DIFFRACTIONr_chiral_restr0.1090.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217171
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 102 -
Rwork0.364 1962 -
obs--64.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33330.68970.29330.64430.25470.5521-0.2950.24920.208-0.20490.11620.189-0.06430.11710.17880.1764-0.0548-0.09660.16810.02090.150720.832-1.497624.9239
21.8860.47390.24450.16820.04330.0548-0.1630.04260.1715-0.01180.0870.057-0.0231-0.03070.07610.17780.0162-0.06020.106900.237411.27773.737539.4286
30.2896-0.33220.48821.2551-0.41490.91370.09580.0744-0.07920.08080.010.09840.07970.2028-0.10580.2162-0.0062-0.07070.1982-0.01190.135616.24-6.7097-7.7082
40.3069-0.50550.67261.5144-0.83331.6417-0.15950.27910.05530.2746-0.11090.0297-0.51970.76560.27040.2574-0.2432-0.14580.47520.12380.120931.04733.8149-6.3666
50.3878-0.0943-0.31410.48410.14710.40240.00660.01570.03510.0419-0.0254-0.0763-0.0936-0.05370.01880.15910.0147-0.02290.1861-0.0060.1078-5.3341-13.4655-28.3092
60.2746-0.2707-0.24770.41120.43260.49220.0130.0040.00120.10640.0433-0.0030.18520.0419-0.05630.22080.0097-0.05070.1676-0.00360.15512.3187-29.5741-24.2624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 214
2X-RAY DIFFRACTION2B1 - 217
3X-RAY DIFFRACTION3C1 - 216
4X-RAY DIFFRACTION4D2 - 217
5X-RAY DIFFRACTION5E3 - 216
6X-RAY DIFFRACTION6F2 - 218

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