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- PDB-2r2e: Crystal structure of S25-2 Fab in complex with Kdo analogues -

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Basic information

Entry
Database: PDB / ID: 2r2e
TitleCrystal structure of S25-2 Fab in complex with Kdo analogues
Components
  • Fab, antibody fragment (IgG1k), heavy chain
  • Fab, antibody fragment (IgG1k), light chain
KeywordsIMMUNE SYSTEM / Fab / anti-carbohydrate antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-KDE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBrooks, C.L. / Evans, S.V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.
Authors: Brooks, C.L. / Muller-Loennies, S. / Brade, L. / Kosma, P. / Hirama, T. / MacKenzie, C.R. / Brade, H. / Evans, S.V.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Fab, antibody fragment (IgG1k), light chain
B: Fab, antibody fragment (IgG1k), heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6323
Polymers48,3542
Non-polymers2781
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 81.170, 132.360
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 Fab, antibody fragment (IgG1k), light chain


Mass: 24242.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab, antibody fragment (IgG1k), heavy chain


Mass: 24110.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#3: Sugar ChemComp-KDE / prop-2-en-1-yl 3-deoxy-beta-L-gulo-oct-2-ulopyranosidonic acid / ALPHA-7-EPI-(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL / prop-2-en-1-yl 3-deoxy-beta-L-gulo-oct-2-ulosidonic acid / prop-2-en-1-yl 3-deoxy-L-gulo-oct-2-ulosidonic acid / prop-2-en-1-yl 3-deoxy-gulo-oct-2-ulosidonic acid


Type: D-saccharide / Mass: 278.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 31, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→19.87 Å / Num. obs: 17962 / % possible obs: 95.5 % / Redundancy: 4.16 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.4-2.493.950.213498.2
2.49-2.593.990.1794.798
2.59-2.74.010.1545.697.6
2.7-2.844.10.122797.7
2.84-3.024.150.0968.697.1
3.02-3.254.230.07511.496.6
3.25-3.584.310.05915.695.8
3.58-4.094.280.05317.694.1
4.09-5.144.320.04522.592.9
5.14-19.874.270.04224.587.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.87 Å
Translation2.5 Å19.87 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.87 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU B: 10.466 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.65 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30618 921 5.1 %RANDOM
Rwork0.24339 ---
obs0.24673 17037 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 19 87 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9574755
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1185438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55123.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98215561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1481518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22293
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4040.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6781.52261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16423557
X-RAY DIFFRACTIONr_scbond_it1.40731462
X-RAY DIFFRACTIONr_scangle_it2.0984.51198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 61 -
Rwork0.279 1247 -
obs--97.98 %

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