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- PDB-4mau: Crystal structure of anti-ST2L antibody C2244 -

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Basic information

Entry
Database: PDB / ID: 4mau
TitleCrystal structure of anti-ST2L antibody C2244
Components
  • C2244 heavy chain
  • C2244 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / FORMIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: Antibody modeling assessment II. Structures and models.
Authors: Teplyakov, A. / Luo, J. / Obmolova, G. / Malia, T.J. / Sweet, R. / Stanfield, R.L. / Kodangattil, S. / Almagro, J.C. / Gilliland, G.L.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Sep 20, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: C2244 light chain
H: C2244 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8119
Polymers48,2052
Non-polymers6077
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-43 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.680, 113.360, 128.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody C2244 light chain


Mass: 23735.400 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody C2244 heavy chain


Mass: 24469.113 Da / Num. of mol.: 1 / Fragment: FD, SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 411 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsHEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A MOUSE VARIABLE DOMAIN AND HUMAN ...HEAVY AND LIGHT CHAINS ARE CHIMERIC MOLECULES EACH COMPRISING A MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN.

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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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 2.3 M ammonium sulfate, 5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 12, 2010 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 49460 / Num. obs: 49460 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 37.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 6.4 / % possible all: 94.4

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1IBG AND 1F8T

1ibg

1f8t


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.775 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21746 1272 2.6 %RANDOM
Rwork0.18374 ---
all0.18462 48187 --
obs0.18462 48187 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 37 404 3700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023396
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9594623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43924.621132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00615532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7121510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212534
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 74 -
Rwork0.228 3154 -
obs--94.4 %

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