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- PDB-3oke: Crystal structure of S25-39 in complex with Ko -

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Basic information

Entry
Database: PDB / ID: 3oke
TitleCrystal structure of S25-39 in complex with Ko
Components
  • S25-39 Fab (IgG1k) heavy chain
  • S25-39 Fab (IgG1k) light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / IgG / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-KO2
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBlackler, R.J. / Evans, S.V.
CitationJournal: Biochemistry / Year: 2011
Title: A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.
Authors: Blackler, R.J. / Brooks, C.L. / Evans, D.W. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionAug 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: 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.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S25-39 Fab (IgG1k) light chain
B: S25-39 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4794
Polymers48,1202
Non-polymers3602
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-44 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.959, 81.245, 127.710
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 S25-39 Fab (IgG1k) light chain


Mass: 24182.846 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 S25-39 Fab (IgG1k) heavy chain


Mass: 23936.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Sugar ChemComp-KO2 / prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulopyranosidonic acid


Type: D-saccharide, alpha linking / Mass: 294.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H18O9
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 289 K / Method: hanging drop / pH: 6.5
Details: PEG 3350, MPD, ZnAc, NaCacod, pH 6.5, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 16, 2010 / Details: OSMIC BLUE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→19.88 Å / Num. obs: 18047 / % possible obs: 95.2 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.4-2.494.20.333.399.2
2.49-2.594.240.2833.799.4
2.59-2.74.250.2494.199
2.7-2.844.20.192598.9
2.84-3.024.130.146.898.4
3.02-3.253.970.1078.498.2
3.25-3.583.720.07810.894.3
3.58-4.093.420.06412.989.4
4.09-5.143.030.05513.882.6
5.14-19.883.170.04417.192.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.1 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.88 Å
Translation2.5 Å19.88 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.356 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 927 5.15 %
Rwork0.2211 --
obs0.2246 18006 95.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.654 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2276 Å20 Å20 Å2
2--0.181 Å20 Å2
3---0.0466 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 21 99 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093436
X-RAY DIFFRACTIONf_angle_d1.1824673
X-RAY DIFFRACTIONf_dihedral_angle_d15.4461230
X-RAY DIFFRACTIONf_chiral_restr0.073529
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4005-2.52680.37461410.2872477X-RAY DIFFRACTION99
2.5268-2.68470.37961400.29642499X-RAY DIFFRACTION99
2.6847-2.89130.36011270.27282520X-RAY DIFFRACTION99
2.8913-3.18120.33821260.25522502X-RAY DIFFRACTION98
3.1812-3.63880.28961260.22192428X-RAY DIFFRACTION95
3.6388-4.57450.23181320.18072221X-RAY DIFFRACTION86
4.5745-19.35620.26361350.19612432X-RAY DIFFRACTION90

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