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- PDB-4ebq: Fab structure of anti-Vaccinia virus D8L antigen mouse IgG2a LA5 -

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Basic information

Entry
Database: PDB / ID: 4ebq
TitleFab structure of anti-Vaccinia virus D8L antigen mouse IgG2a LA5
Components(anti-Vaccinia D8L antigen monoclonal IgG2a antibody LA5, ...) x 2
KeywordsIMMUNE SYSTEM / variable domain / constant domain / CDR / hypervariable region / neutralizing antibody / vaccinia virus / D8L envelope protein / conformational epitope / discontinuous epitope / D8L antigen binding / neutralizing mAb in presence of complement / D8L vaccinia envelope protein / papain treatment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMatho, M.H. / Zajonc, D.M.
CitationJournal: J.Virol. / Year: 2012
Title: Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition by the Antibody LA5.
Authors: Matho, M.H. / Maybeno, M. / Benhnia, M.R. / Becker, D. / Meng, X. / Xiang, Y. / Crotty, S. / Peters, B. / Zajonc, D.M.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...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 / 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

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Assembly

Deposited unit
H: anti-Vaccinia D8L antigen monoclonal IgG2a antibody LA5, heavy chain
L: anti-Vaccinia D8L antigen monoclonal IgG2a antibody LA5, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7008
Polymers47,3172
Non-polymers3826
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-52 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.190, 93.360, 135.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody anti-Vaccinia D8L antigen monoclonal IgG2a antibody LA5, heavy chain


Mass: 23967.729 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: splenocytes fused with mouse myeloma SP2/0 cells
Cell: Hybridoma / Gene: IgG2a, VAR-gene, heavy chain
#2: Antibody anti-Vaccinia D8L antigen monoclonal IgG2a antibody LA5, light chain


Mass: 23349.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: splenocytes fused with mouse myeloma SP2/0 cells
Cell: Hybridoma / Gene: IgG2a, VAR-gene, light chain

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Non-polymers , 5 types, 416 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 10% w/v PEG3000, 100 mM phosphate/citrate, 200 mM sodium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.100002 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2010 / Details: mirrors
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.100002 Å / Relative weight: 1
ReflectionResolution: 1.6→135.96 Å / Num. all: 60567 / Num. obs: 59711 / % possible obs: 96.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.048 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.695.10.3232.44243883310.32393.8
1.69-1.795.20.2113.64155780440.21195.3
1.79-1.915.40.1455.14115576520.14596.5
1.91-2.075.60.0987.24029772430.09898.1
2.07-2.265.80.0857.63860666940.08597.3
2.26-2.535.90.06310.63597761200.06398.9
2.53-2.925.60.049133040354240.04998.1
2.92-3.585.90.03616.12623944170.03693.9
3.58-5.066.10.0319.82227436740.0399.3
5.06-31.125.60.02621.61179921120.02697.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.29 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.34 Å
Translation2.5 Å30.34 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NSN

1nsn


Resolution: 1.6→31.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2287 / WRfactor Rwork: 0.1982 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8502 / SU B: 4.183 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0992 / SU Rfree: 0.0979 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 3019 5.1 %RANDOM
Rwork0.1982 ---
obs0.1998 59691 96.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.77 Å2 / Biso mean: 24.4607 Å2 / Biso min: 8.17 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 21 410 3709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223514
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9554817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38323.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22115558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9581516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212675
X-RAY DIFFRACTIONr_mcbond_it0.6151.52220
X-RAY DIFFRACTIONr_mcangle_it1.06723627
X-RAY DIFFRACTIONr_scbond_it1.78531294
X-RAY DIFFRACTIONr_scangle_it2.4944.51176
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 224 -
Rwork0.272 3988 -
all-4212 -
obs--92.51 %
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)
11.53070.1149-0.21032.12711.01944.9012-0.1205-0.0906-0.14850.28140.10680.0380.43630.01420.01360.1890.03940.05960.11590.03410.114-26.228-7.56156.803
22.97662.0824-1.39333.566-1.33242.4045-0.03980.0490.02460.0197-0.0398-0.0480.07790.03530.07960.00750.01010.00310.044-0.00510.0647-8.268-4.59527.672
30.95460.6013-1.84884.5545-2.59764.3359-0.0544-0.02620.05030.47170.22690.2946-0.1972-0.1763-0.17240.14710.07360.05780.12770.01450.1287-31.60912.74650.52
41.5562-1.1355-1.34923.08392.04283.85240.04220.21460.0085-0.0344-0.11070.10360.0547-0.26370.06850.0069-0.00470.00220.06930.01960.0738-18.2273.81820.953
55.3283-3.0686-2.638811.95514.96648.12560.21760.52350.0977-0.4644-0.1617-0.1095-0.0363-0.3812-0.05590.04930.0053-0.01870.18050.03720.033-15.7083.0678.672
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 115
2X-RAY DIFFRACTION2H116 - 222
3X-RAY DIFFRACTION3L2 - 109
4X-RAY DIFFRACTION4L110 - 186
5X-RAY DIFFRACTION5L187 - 214

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