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- PDB-7t0f: Crystal structure of S25-39 Fab in complex with 4-MeO-KdoOAll -

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Basic information

Entry
Database: PDB / ID: 7t0f
TitleCrystal structure of S25-39 Fab in complex with 4-MeO-KdoOAll
Components
  • S25-39 Fab heavy chain
  • S25-39 Fab light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Carbohydrate / Induced fit / Conformational selection
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-K71
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLegg, M.S.G. / Blackler, R.J. / Evans, S.V.
Funding support Austria, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Austria
Austrian Science FundP 24021 Austria
Austrian Science FundP 26919 Austria
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Antigen binding by conformational selection in near-germline antibodies.
Authors: Blackler, R.J. / Muller-Loennies, S. / Pokorny-Lehrer, B. / Legg, M.S.G. / Brade, L. / Brade, H. / Kosma, P. / Evans, S.V.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: S25-39 Fab heavy chain
L: S25-39 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5443
Polymers48,2922
Non-polymers2521
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-20 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.111, 63.624, 61.636
Angle α, β, γ (deg.)90.000, 97.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody S25-39 Fab heavy chain


Mass: 24051.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody S25-39 Fab light chain


Mass: 24239.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Description: hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-K71 / 3-deoxy-4-O-methyl-alpha-D-manno-oct-2-ulopyranosonic acid


Mass: 252.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001, 5 mM 4-O-methyl-KdoOAll

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27284 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.042 / Rrim(I) all: 0.083 / Χ2: 0.989 / Net I/σ(I): 10.9 / Num. measured all: 95425
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0730.39826000.8530.2480.4720.74795.1
2.07-2.153.40.33627170.890.2070.3970.75999.6
2.15-2.253.50.26627150.9240.1610.3120.7499.9
2.25-2.373.60.21927640.9420.1330.2570.79199.8
2.37-2.523.60.18127370.9570.1090.2120.89499.9
2.52-2.713.60.1327280.9790.0780.1530.94399.8
2.71-2.993.70.08927490.9860.0530.1041.07299.7
2.99-3.423.60.06327410.9930.0370.0731.33499.2
3.42-4.313.50.0527360.9940.0290.0581.30598.8
4.31-503.50.04627970.9920.0270.0531.22298.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKD

3okd


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.152 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 1270 5 %RANDOM
Rwork0.2144 ---
obs0.2169 24109 91.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.24 Å2 / Biso mean: 27.783 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.38 Å2
2---0.21 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 17 151 3498
Biso mean--27.21 27.82 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023429
X-RAY DIFFRACTIONr_bond_other_d0.0020.023132
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.954662
X-RAY DIFFRACTIONr_angle_other_deg0.8243.0027247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2595428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14223.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15315550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4581517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
LS refinement shellResolution: 2→2.036 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.395 46 -
Rwork0.267 950 -
obs--49.23 %

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