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- PDB-2xza: Crystal Structure of recombinant A.17 antibody FAB fragment -

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Basic information

Entry
Database: PDB / ID: 2xza
TitleCrystal Structure of recombinant A.17 antibody FAB fragment
Components
  • FAB A.17 HEAVY CHAIN
  • FAB A.17 LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å
AuthorsCarletti, E. / Nachon, F. / Nicolet, Y. / Masson, P. / Kurkova, I. / Smirnov, I. / Friboulet, A. / Tramontano, A. / Gabibov, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Reactibodies Generated by Kinetic Selection Couple Chemical Reactivity with Favorable Protein Dynamics.
Authors: Smirnov, I. / Carletti, E. / Kurkova, I. / Nachon, F. / Nicolet, Y. / Mitkevich, V.A. / Debat, H. / Avalle, B. / Belogurov, A.A. / Kuznetsov, N. / Reshetnyak, A. / Masson, P. / Tonevitsky, A. ...Authors: Smirnov, I. / Carletti, E. / Kurkova, I. / Nachon, F. / Nicolet, Y. / Mitkevich, V.A. / Debat, H. / Avalle, B. / Belogurov, A.A. / Kuznetsov, N. / Reshetnyak, A. / Masson, P. / Tonevitsky, A.G. / Ponomarenko, N. / Makarov, A.A. / Friboulet, A. / Tramontano, A. / Gabibov, A.
History
DepositionNov 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
H: FAB A.17 HEAVY CHAIN
L: FAB A.17 LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,4632
Polymers46,4632
Non-polymers00
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-20.7 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.150, 66.710, 66.100
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB A.17 HEAVY CHAIN


Mass: 23322.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster)
#2: Antibody FAB A.17 LIGHT CHAIN


Mass: 23140.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.3 Å3/Da / Density % sol: 47.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M ADA BUFFER PH 6.5 0.1M MGCL2 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 68859 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 23.8
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 3.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.5→7.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.492 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21095 2053 3 %RANDOM
Rwork0.16623 ---
obs0.16759 66403 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.742 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 0 0 659 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0223398
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3781.9634670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69725.323124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.023157
X-RAY DIFFRACTIONr_chiral_restr0.1780.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212593
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_it1.6241.52201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.60323591
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.49331197
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3094.51065
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 147 -
Rwork0.264 4775 -
obs--99.31 %

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