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- PDB-4lci: Anti canine CD28 antibody, 1C6 -

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Basic information

Entry
Database: PDB / ID: 4lci
TitleAnti canine CD28 antibody, 1C6
Components(anti canine CD28 antibody, 1C6, ...) x 2
KeywordsIMMUNE SYSTEM / Immunoglobulin / antibody / CD28
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / FORMIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGewe, M.M. / Rupert, P.B. / Strong, R.K.
CitationJournal: To be Published
Title: Anti canine CD28 antibody, 1C6
Authors: Gewe, M.M. / Rupert, P.B. / Strong, R.K.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Source and taxonomy
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 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
L: anti canine CD28 antibody, 1C6, light chain
H: anti canine CD28 antibody, 1C6, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9359
Polymers26,5442
Non-polymers3917
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-20 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.599, 71.621, 73.234
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody anti canine CD28 antibody, 1C6, light chain


Mass: 12979.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22(B)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Antibody anti canine CD28 antibody, 1C6, heavy chain


Mass: 13564.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22(b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 173 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3.5M Sodium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→44.6 Å / Num. obs: 18024 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.38 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1748 / Rsym value: 0.291 / % possible all: 94.99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H8N

1h8n


Resolution: 1.9→44.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.704 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23038 986 5.1 %RANDOM
Rwork0.17903 ---
obs0.18157 18024 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.736 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1840 0 25 166 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191929
X-RAY DIFFRACTIONr_bond_other_d0.0010.021736
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9472620
X-RAY DIFFRACTIONr_angle_other_deg0.7673.0024003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0685243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01523.5881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79815296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.976158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 65 -
Rwork0.245 1240 -
obs--93.82 %

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