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- PDB-3okm: Crystal structure of unliganded S25-39 -

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Basic information

Entry
Database: PDB / ID: 3okm
TitleCrystal structure of unliganded S25-39
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
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 25, 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 1.3Nov 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _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: S25-39 Fab (IgG1k) light chain
B: S25-39 Fab (IgG1k) heavy chain


Theoretical massNumber of molelcules
Total (without water)48,2062
Polymers48,2062
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-21 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.015, 83.188, 69.500
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211

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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: 24022.961 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.: 175 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
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 8, 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→19.91 Å / Num. obs: 16790 / % possible obs: 92.6 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.4-2.492.980.2153.186.4
2.49-2.592.980.2033.484.9
2.59-2.72.920.1923.688.6
2.7-2.842.90.1733.988.9
2.84-3.022.860.1584.491.8
3.02-3.252.880.1265.695.8
3.25-3.582.970.1137.196.9
3.58-4.093.050.0969.596.8
4.09-5.143.040.07614.197.4
5.14-19.912.930.06716.897.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.74 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.91 Å
Translation2.5 Å19.91 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→19.766 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.42 / σ(F): 1.48 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3062 846 5.04 %
Rwork0.2287 --
obs0.2324 16788 92.55 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.431 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2572 Å2-0 Å2-0.1318 Å2
2---0.234 Å20 Å2
3---0.4912 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3272 0 0 175 3447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043362
X-RAY DIFFRACTIONf_angle_d0.8194578
X-RAY DIFFRACTIONf_dihedral_angle_d14.6051184
X-RAY DIFFRACTIONf_chiral_restr0.055517
X-RAY DIFFRACTIONf_plane_restr0.003582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.55030.46011300.35582446X-RAY DIFFRACTION86
2.5503-2.74670.36231500.30052480X-RAY DIFFRACTION87
2.7467-3.02230.35911360.25832597X-RAY DIFFRACTION91
3.0223-3.45760.32841380.23492787X-RAY DIFFRACTION96
3.4576-4.34850.3011530.2132777X-RAY DIFFRACTION97
4.3485-19.76690.23481390.18952855X-RAY DIFFRACTION97

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