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- PDB-5dqj: Structure of unliganded S55-5 Fab -

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Basic information

Entry
Database: PDB / ID: 5dqj
TitleStructure of unliganded S55-5 Fab
Components
  • S55-5 Fab (IgG1 kappa) light chain
  • S55-5 Fab (IgG1) heavy chain
KeywordsIMMUNE SYSTEM / antibody / Fab / carbohydrate binding / Phospholipid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from unrelated V-genes
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Rodriguez, T. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: S55-5 Fab (IgG1 kappa) light chain
H: S55-5 Fab (IgG1) heavy chain
B: S55-5 Fab (IgG1 kappa) light chain
A: S55-5 Fab (IgG1) heavy chain


Theoretical massNumber of molelcules
Total (without water)95,8694
Polymers95,8694
Non-polymers00
Water97354
1
L: S55-5 Fab (IgG1 kappa) light chain
H: S55-5 Fab (IgG1) heavy chain


Theoretical massNumber of molelcules
Total (without water)47,9342
Polymers47,9342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-21 kcal/mol
Surface area19670 Å2
MethodPISA
2
B: S55-5 Fab (IgG1 kappa) light chain
A: S55-5 Fab (IgG1) heavy chain


Theoretical massNumber of molelcules
Total (without water)47,9342
Polymers47,9342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-21 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.607, 139.872, 72.076
Angle α, β, γ (deg.)90.000, 110.660, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21B
12H
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010L1 - 217
2010B1 - 217
1020H1 - 222
2020A1 - 222

NCS ensembles :
ID
1
2

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Components

#1: Antibody S55-5 Fab (IgG1 kappa) light chain


Mass: 24087.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#2: Antibody S55-5 Fab (IgG1) heavy chain


Mass: 23846.869 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 5% (w/v) glycerol and 15% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2011 / Details: Vertical focusing mirror
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 30002 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Χ2: 0.909 / Net I/av σ(I): 18.743 / Net I/σ(I): 17 / Num. measured all: 111916
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.693.80.61930340.8230.3670.7210.995100
2.69-2.83.80.42630290.9040.2520.4951100
2.8-2.933.80.25929930.950.1540.3011.006100
2.93-3.083.80.17129880.9760.1020.20.986100
3.08-3.273.80.11130150.9890.0670.130.91299.9
3.27-3.533.80.07730080.9930.0470.0910.89899.7
3.53-3.883.50.06128720.9940.0380.0720.96595.4
3.88-4.443.60.03829980.9980.0240.0450.66198.6
4.44-5.583.70.0330070.9980.0180.0350.75699.4
5.58-253.70.02930580.9980.0170.0330.88799.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DQD

5dqd


Resolution: 2.61→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2414 / WRfactor Rwork: 0.1981 / FOM work R set: 0.8206 / SU B: 11.116 / SU ML: 0.232 / SU R Cruickshank DPI: 1.1244 / SU Rfree: 0.2959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.124 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1461 4.9 %RANDOM
Rwork0.1932 ---
obs0.1949 28504 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120 Å2 / Biso mean: 67.347 Å2 / Biso min: 31.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å2-0 Å24.08 Å2
2---2.57 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 2.61→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 0 54 6772
Biso mean---57.78 -
Num. residues----878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196882
X-RAY DIFFRACTIONr_bond_other_d0.0040.026300
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9439354
X-RAY DIFFRACTIONr_angle_other_deg0.954314574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09323.741278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.52151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1031540
X-RAY DIFFRACTIONr_chiral_restr0.0770.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217754
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021554
X-RAY DIFFRACTIONr_mcbond_it4.0866.5553508
X-RAY DIFFRACTIONr_mcbond_other4.0856.5543507
X-RAY DIFFRACTIONr_mcangle_it6.3049.8314378
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L111510.15
12B111510.15
21H118240.11
22A118240.11
LS refinement shellResolution: 2.606→2.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 100 -
Rwork0.32 2033 -
all-2133 -
obs--95.22 %

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