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- PDB-6apc: Crystal Structure of Infant Antibody ADI-19425 -

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Basic information

Entry
Database: PDB / ID: 6apc
TitleCrystal Structure of Infant Antibody ADI-19425
Components
  • Epididymis luminal protein 214
  • IGL@ protein
KeywordsIMMUNE SYSTEM / viral fusion glycoprotein / immunoglobulin / respiratory syncytial virus
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
CitationJournal: Immunity / Year: 2018
Title: Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation.
Authors: Goodwin, E. / Gilman, M.S.A. / Wrapp, D. / Chen, M. / Ngwuta, J.O. / Moin, S.M. / Bai, P. / Sivasubramanian, A. / Connor, R.I. / Wright, P.F. / Graham, B.S. / McLellan, J.S. / Walker, L.M.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
H: Epididymis luminal protein 214
L: IGL@ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0294
Polymers46,8372
Non-polymers1922
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-46 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.230, 66.530, 125.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Epididymis luminal protein 214


Mass: 23881.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEL-214 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#2: Antibody IGL@ protein /


Mass: 22955.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Cell (production host): FreeStyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 nL of ADI-19425 Fab at 8.78 mg/ml, 50 nL of crystal seed solution, and 100 nL of reservoir solution containing 1.5 M Ammonium sulfate, 0.1 M sodium chloride, and 0.1 M BisTris pH 6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→26.07 Å / Num. obs: 57347 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.735.50.32829400.930.1530.36399.4
9-26.074.90.0794400.990.0380.08895.6

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.5.17data scaling
PHENIX1.11.1refinement
PDB_EXTRACT3.22data extraction
PHASER2.5.7phasing
Coot0.8.6.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EYQ, 3H42

3eyq

3h42


Resolution: 1.7→26.07 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.07
RfactorNum. reflection% reflection
Rfree0.2036 2896 5.06 %
Rwork0.1742 --
obs0.1757 57181 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.18 Å2 / Biso mean: 18.44 Å2 / Biso min: 6.12 Å2
Refinement stepCycle: final / Resolution: 1.7→26.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 10 692 3935
Biso mean--21.28 30.15 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033326
X-RAY DIFFRACTIONf_angle_d0.6674538
X-RAY DIFFRACTIONf_chiral_restr0.049509
X-RAY DIFFRACTIONf_plane_restr0.005577
X-RAY DIFFRACTIONf_dihedral_angle_d12.5391973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72790.19381280.18652517264599
1.7279-1.75770.22851440.18222552269699
1.7577-1.78960.21381240.183325532677100
1.7896-1.8240.21371300.177625402670100
1.824-1.86120.20591170.173725892706100
1.8612-1.90170.22361300.19712551268199
1.9017-1.94590.23511320.223225442676100
1.9459-1.99460.21241270.175525932720100
1.9946-2.04850.19741430.167525562699100
2.0485-2.10870.1931340.164225932727100
2.1087-2.17680.20291360.169625652701100
2.1768-2.25450.23721550.22752531268699
2.2545-2.34470.23481420.18922534267698
2.3447-2.45140.22591490.181825842733100
2.4514-2.58050.20621180.180526212739100
2.5805-2.7420.19921390.183625842723100
2.742-2.95350.20111390.177725902729100
2.9535-3.25020.22881710.171126082779100
3.2502-3.71930.15921390.152826262765100
3.7193-4.68150.18551330.137326822815100
4.6815-26.07580.18461660.17627722938100
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)
10.58630.1348-1.13090.3422-0.21043.2007-0.05340.065-0.0287-0.07320.0444-0.02430.1813-0.06850.01470.0678-0.00290.00960.0877-0.01110.10048.1649-20.4347-3.0751
21.2910.5842-0.3853.94291.10533.2760.093-0.07890.06640.13640.00030.1036-0.0214-0.1011-0.08760.06280.0059-0.00810.09160.01960.1124-6.4215-18.076333.1171
31.7789-0.6237-0.69681.37940.77751.38280.05930.07980.1322-0.1617-0.0116-0.0156-0.2407-0.1477-0.04360.11370.0418-0.00170.09650.00740.11097.05640.84951.6258
40.7784-0.08150.37592.0192-0.67221.7484-0.00260.0059-0.01790.0828-0.1405-0.172-0.04230.08180.11080.05560.0067-0.00690.08550.00950.1145.9329-9.939126.2186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resid 2:123H2 - 123
2X-RAY DIFFRACTION2chain H and resid 124:214H124 - 214
3X-RAY DIFFRACTION3chain L and resid 4:111L4 - 111
4X-RAY DIFFRACTION4chain L and resid 113:209L113 - 209

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