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- PDB-4hxa: Crystal structure of 13D9 FAB -

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Basic information

Entry
Database: PDB / ID: 4hxa
TitleCrystal structure of 13D9 FAB
Components
  • 13D9 FAB HEAVY CHAIN
  • 13D9 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTIBODY / FAB / CARBOHYDRATE / COMPLEMENTARITY DETERMINING REGIONS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsJohal, A.R. / Jarrell, H.C. / Khieu, N.H. / Letts, J.A. / Landry, R.C. / Jachymek, W. / Yang, Q. / Jennings, H.J. / Brisson, J.R. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2013
Title: The antigen-binding site of an N-propionylated polysialic acid-specific antibody protective against group B meningococci is consistent with extended epitopes.
Authors: Johal, A.R. / Jarrell, H.C. / Letts, J.A. / Khieu, N.H. / Landry, R.C. / Jachymek, W. / Yang, Q. / Jennings, H.J. / Brisson, J.R. / Evans, S.V.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 13D9 FAB LIGHT CHAIN
H: 13D9 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,2452
Polymers47,2452
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-19 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.750, 100.280, 132.190
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 13D9 FAB LIGHT CHAIN


Mass: 23280.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ASCITES / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C
#2: Antibody 13D9 FAB HEAVY CHAIN


Mass: 23963.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ASCITES / Source: (natural) MUS MUSCULUS (house mouse) / Strain: BALB/C
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 10000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 19, 2006 / Details: OSMIC BLUE MIRRORS
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. obs: 31114 / % possible obs: 88.4 % / Redundancy: 4.67 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.8 / % possible all: 91.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB FROM YST9.1

Resolution: 2.06→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.884 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1556 5 %RANDOM
Rwork0.213 ---
obs0.217 31104 88.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å20 Å20 Å2
2---1.31 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 0 361 3676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223442
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.9494691
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6135437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96323.806134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08215557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1741517
X-RAY DIFFRACTIONr_chiral_restr0.1660.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022589
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21541
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22282
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2281.52238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95423549
X-RAY DIFFRACTIONr_scbond_it2.8931416
X-RAY DIFFRACTIONr_scangle_it4.0044.51142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 106 -
Rwork0.257 2226 -
obs--92.03 %

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