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- PDB-3okd: Crystal structure of S25-39 in complex with Kdo -

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Basic information

Entry
Database: PDB / ID: 3okd
TitleCrystal structure of S25-39 in complex with Kdo
Components(S25-39 Fab (IgG1k) ...) x 2
KeywordsIMMUNE SYSTEM / antibody / Fab / IgG / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.source
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
A: S25-39 Fab (IgG1k) light chain
B: S25-39 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6366
Polymers48,1202
Non-polymers5164
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-40 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.747, 82.011, 131.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules AB

#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

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O8
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 595 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.19 %
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: May 27, 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: 1.8→19.98 Å / Num. obs: 46591 / % possible obs: 99.4 % / Redundancy: 3.65 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
1.8-1.863.420.2973.2100
1.86-1.943.610.2363.9100
1.94-2.033.630.1764.9100
2.03-2.133.70.146.1100
2.13-2.273.750.1167.299.9
2.27-2.443.770.0998.599.9
2.44-2.693.770.0810.399.9
2.69-3.073.740.06112.799.5
3.07-3.873.670.04917.198.3
3.87-19.983.490.04520.896.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.39 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.98 Å
Translation2.5 Å19.98 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: 1.8→19.976 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 2359 5.06 %
Rwork0.2333 --
obs0.2355 46576 99.34 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.865 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4212 Å2-0 Å2-0 Å2
2---0.0291 Å2-0 Å2
3----0.3921 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 31 592 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093470
X-RAY DIFFRACTIONf_angle_d1.2434713
X-RAY DIFFRACTIONf_dihedral_angle_d13.2471246
X-RAY DIFFRACTIONf_chiral_restr0.083531
X-RAY DIFFRACTIONf_plane_restr0.005598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83680.4071560.36062600X-RAY DIFFRACTION100
1.8368-1.87670.41491450.32562522X-RAY DIFFRACTION100
1.8767-1.92030.3411320.29692611X-RAY DIFFRACTION100
1.9203-1.96830.33721320.242568X-RAY DIFFRACTION100
1.9683-2.02140.27131410.24542577X-RAY DIFFRACTION100
2.0214-2.08090.29461300.22922608X-RAY DIFFRACTION100
2.0809-2.1480.29331350.23032576X-RAY DIFFRACTION100
2.148-2.22460.29431260.23092620X-RAY DIFFRACTION100
2.2246-2.31360.28431480.23182572X-RAY DIFFRACTION100
2.3136-2.41870.27341410.22712605X-RAY DIFFRACTION100
2.4187-2.5460.28071340.23652618X-RAY DIFFRACTION100
2.546-2.70510.26111460.23382584X-RAY DIFFRACTION100
2.7051-2.91340.27411360.22622615X-RAY DIFFRACTION100
2.9134-3.20550.26481270.22312625X-RAY DIFFRACTION99
3.2055-3.66690.25271100.22412636X-RAY DIFFRACTION98
3.6669-4.61050.23331690.20892577X-RAY DIFFRACTION97
4.6105-19.97710.28751510.24372703X-RAY DIFFRACTION96

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