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- PDB-6a76: Crystal structure of the Fab fragment of B5209B, a murine monoclo... -

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Basic information

Entry
Database: PDB / ID: 6a76
TitleCrystal structure of the Fab fragment of B5209B, a murine monoclonal antibody specific for the fifth immunoglobulin domain (Ig5) of human ROBO1
Components
  • Heavy chain of the anti-human Robo1 antibody B5209B Fab
  • Light chain of the anti-human Robo1 antibody B5209B Fab
KeywordsIMMUNE SYSTEM / hepatocellular carcinoma antigen / angiogenesis / antibody drug
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMizohata, E. / Nakayama, T. / Kado, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Council for Science and Technology PolicyFirst Program-MDADD Japan
CitationJournal: Structure / Year: 2019
Title: Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.
Authors: Yamashita, T. / Mizohata, E. / Nagatoishi, S. / Watanabe, T. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Nakayama, T. / Kado, Y. / Yokota, Y. / Matsumura, H. / Kawamura, T. / Kodama, T. / ...Authors: Yamashita, T. / Mizohata, E. / Nagatoishi, S. / Watanabe, T. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Nakayama, T. / Kado, Y. / Yokota, Y. / Matsumura, H. / Kawamura, T. / Kodama, T. / Hamakubo, T. / Inoue, T. / Fujitani, H. / Tsumoto, K.
History
DepositionJul 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Oct 9, 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
L: Light chain of the anti-human Robo1 antibody B5209B Fab
H: Heavy chain of the anti-human Robo1 antibody B5209B Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2469
Polymers46,5982
Non-polymers6497
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-41 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.431, 83.947, 129.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Light chain of the anti-human Robo1 antibody B5209B Fab


Mass: 23098.506 Da / Num. of mol.: 1
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 Heavy chain of the anti-human Robo1 antibody B5209B Fab


Mass: 23499.217 Da / Num. of mol.: 1
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: 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM sodium cacodylate trihydrate (pH 6.5), 29% (w/v) PEG 8000, 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 73816 / % possible obs: 99 % / Redundancy: 6.5 % / Net I/σ(I): 24.9
Reflection shellResolution: 1.5→1.55 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.484 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1651 3752 5.1 %RANDOM
Rwork0.12917 ---
obs0.13095 70018 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.692 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2--1.23 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 41 359 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.023410
X-RAY DIFFRACTIONr_bond_other_d0.0020.023014
X-RAY DIFFRACTIONr_angle_refined_deg2.5991.9594645
X-RAY DIFFRACTIONr_angle_other_deg1.9563.0027050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2175440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74424.252127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27415538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2281513
X-RAY DIFFRACTIONr_chiral_restr0.3380.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213778
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02671
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_it4.8552.551739
X-RAY DIFFRACTIONr_mcbond_other4.8482.5491738
X-RAY DIFFRACTIONr_mcangle_it5.2623.8282183
X-RAY DIFFRACTIONr_mcangle_other5.2633.832184
X-RAY DIFFRACTIONr_scbond_it6.1282.9841671
X-RAY DIFFRACTIONr_scbond_other6.1342.9861667
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6954.3162456
X-RAY DIFFRACTIONr_long_range_B_refined8.45751.20614020
X-RAY DIFFRACTIONr_long_range_B_other8.45751.20514020
X-RAY DIFFRACTIONr_rigid_bond_restr6.09436424
X-RAY DIFFRACTIONr_sphericity_free41.271595
X-RAY DIFFRACTIONr_sphericity_bonded21.35256606
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 256 -
Rwork0.232 4804 -
obs--92.78 %

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