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

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Basic information

Entry
Database: PDB / ID: 3qcu
TitleCrystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0)
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 / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / Potential therapeutics for SARS / adaptive immune response / 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/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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-NKN / Immunoglobulin kappa constant / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.979 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)96,5226
Polymers95,7574
Non-polymers7652
Water5,116284
1
H: LT3015 antibody Fab fragment, heavy chain
L: LT3015 antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2613
Polymers47,8782
Non-polymers3821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area20410 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)48,2613
Polymers47,8782
Non-polymers3821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-24 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.526, 184.351, 130.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-NKN / (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate / 14:0 LPA / myristoyl lysophosphatidic acid


Mass: 382.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H35O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
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: 1.979→46.749 Å / Num. obs: 72518 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.061 / Χ2: 0.971 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.979-2.017.20.48236130.75199.9
2.01-2.057.50.42535510.774100
2.05-2.097.50.37535930.81100
2.09-2.137.50.30735650.816100
2.13-2.187.50.26836160.856100
2.18-2.237.50.26335950.913100
2.23-2.297.50.22835881.18100
2.29-2.357.50.19735970.913100
2.35-2.427.50.16336260.942100
2.42-2.497.50.1435960.954100
2.49-2.587.50.12336020.992100
2.58-2.697.50.10136281.061100
2.69-2.817.50.08436041.075100
2.81-2.967.50.06936171.135100
2.96-3.147.40.05636311.065100
3.14-3.397.40.04936641.086100
3.39-3.737.40.0536521.034100
3.73-4.267.30.05136621.002100
4.26-5.377.10.03737201.016100
5.37-507.10.02737981.03498.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.34 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å9.99 Å
Translation4 Å9.99 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 3QCT

3qct


Resolution: 1.979→46.749 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2541 / WRfactor Rwork: 0.2223 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8165 / SU B: 9.329 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1852 / SU Rfree: 0.1619 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 3653 5 %RANDOM
Rwork0.2215 ---
all0.223 72568 --
obs0.223 72488 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.1 Å2 / Biso mean: 34.587 Å2 / Biso min: 10.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.979→46.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6686 0 50 284 7020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226910
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9579390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78124.71276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.692151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4261518
X-RAY DIFFRACTIONr_chiral_restr0.080.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215202
X-RAY DIFFRACTIONr_mcbond_it0.6191.54340
X-RAY DIFFRACTIONr_mcangle_it1.14427020
X-RAY DIFFRACTIONr_scbond_it1.71332570
X-RAY DIFFRACTIONr_scangle_it2.7574.52370
LS refinement shellResolution: 1.979→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 275 -
Rwork0.247 5017 -
all-5292 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6433-1.27440.13081.1439-0.01230.7806-0.00140.0257-0.12680.01920.00150.09940.0358-0.2797-0.00010.0598-0.01780.00690.1073-0.00850.027632.9087-34.262113.043
22.2473-0.4714-0.15830.35830.33580.93480.0436-0.15350.14730.0329-0.04110.0229-0.0657-0.3071-0.00250.04330.03410.00790.1266-0.00690.042437.5167-18.829421.6458
32.10631.05280.43071.10940.22120.4954-0.0390.0459-0.07960.00030.0391-0.14670.04850.0943-0.00010.1055-0.00450.05230.0342-0.020.0649.6404-31.6494-12.8709
42.95360.851-0.20530.8324-0.32650.4115-0.0290.24690.0543-0.12970.0192-0.04780.02830.06310.00980.1485-0.01440.02740.0405-0.00140.042447.0607-14.1229-16.8001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H-10 - 9999
2X-RAY DIFFRACTION2L-10 - 9999
3X-RAY DIFFRACTION3I-10 - 9999
4X-RAY DIFFRACTION4M-10 - 9999

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