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- PDB-3qcv: Crystal structure of the LT3015 antibody Fab fragment in complex ... -

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Basic information

Entry
Database: PDB / ID: 3qcv
TitleCrystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (18:2)
Components
  • LT3015 antibody Fab fragment, heavy chain
  • LT3015 antibody Fab fragment, light chain
KeywordsIMMUNE SYSTEM / antibody / lysophosphatidic acid binding
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-18L / Immunoglobulin kappa constant / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsFleming, J.K. / Wojciak, J.M. / Campbell, M.-A. / Huxford, T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Biochemical and structural characterization of lysophosphatidic Acid binding by a humanized monoclonal antibody.
Authors: Fleming, J.K. / Wojciak, J.M. / Campbell, M.A. / Huxford, T.
History
DepositionJan 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: LT3015 antibody Fab fragment, heavy chain
L: LT3015 antibody Fab fragment, light chain
I: LT3015 antibody Fab fragment, heavy chain
M: LT3015 antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6266
Polymers95,7574
Non-polymers8692
Water1,74797
1
H: LT3015 antibody Fab fragment, heavy chain
L: LT3015 antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3133
Polymers47,8782
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area20300 Å2
MethodPISA
2
I: LT3015 antibody Fab fragment, heavy chain
M: LT3015 antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3133
Polymers47,8782
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-24 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.980, 183.131, 127.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody LT3015 antibody Fab fragment, heavy chain


Mass: 24038.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Production host: Cricetulus griseus (Chinese hamster) / References: PDB-3QCT, UniProt: Q6N089
#2: Antibody LT3015 antibody Fab fragment, light chain


Mass: 23839.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Cricetulus griseus (Chinese hamster) / References: PDB-3QCT, UniProt: P01834
#3: Chemical ChemComp-18L / (2R)-2-hydroxy-3-(phosphonooxy)propyl (9Z,12Z)-octadeca-9,12-dienoate / D (+)-sn-1-O-linoleoyl-glyceryl-3-phosphate


Mass: 434.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H39O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.095 M sodium citrate pH 5.6, 19% (v/v) isopropanol, 19% (w/v) PEG 4000, and 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2009
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.966 Å / Num. obs: 34955 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.122 / Χ2: 1.025 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.547.40.47517270.826100
2.54-2.597.50.42317280.859100
2.59-2.647.50.38117010.897100
2.64-2.697.40.35517500.952100
2.69-2.757.50.30317010.986100
2.75-2.827.50.26817441.007100
2.82-2.897.40.24417401.082100
2.89-2.967.50.20217201.123100
2.96-3.057.40.18117261.193100
3.05-3.157.40.15817261.175100
3.15-3.267.40.13917441.086100
3.26-3.397.40.12417391.098100
3.39-3.557.40.1117370.968100
3.55-3.737.40.10217561.045100
3.73-3.977.30.09817471.05100
3.97-4.277.40.09217531.025100
4.27-4.77.30.08817580.998100
4.7-5.387.10.08417771.04100
5.38-6.7870.07817931.06399.9
6.78-5070.07518881.035100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.73 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.51 Å49.97 Å
Translation2.51 Å49.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QCU

3qcu


Resolution: 2.51→49.966 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2605 / WRfactor Rwork: 0.2124 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8065 / SU B: 10.034 / SU ML: 0.225 / SU R Cruickshank DPI: 0.5969 / SU Rfree: 0.3094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.597 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 1754 5 %RANDOM
Rwork0.2149 ---
obs0.2175 34931 99.24 %-
all-35199 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.95 Å2 / Biso mean: 27.9375 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.51→49.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6686 0 58 97 6841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226918
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9589398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60624.71276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.861151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5291518
X-RAY DIFFRACTIONr_chiral_restr0.0770.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215218
X-RAY DIFFRACTIONr_mcbond_it0.5631.54340
X-RAY DIFFRACTIONr_mcangle_it1.08127020
X-RAY DIFFRACTIONr_scbond_it1.44432578
X-RAY DIFFRACTIONr_scangle_it2.5294.52378
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 118 -
Rwork0.272 2200 -
all-2318 -
obs--89.95 %

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