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- PDB-4dn3: Crystal structure of anti-mcp-1 antibody cnto888 -

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Basic information

Entry
Database: PDB / ID: 4dn3
TitleCrystal structure of anti-mcp-1 antibody cnto888
Components
  • CNTO888 HEAVY CHAIN
  • CNTO888 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsObmolova, G. / Teplyakov, A. / Malia, T. / Grygiel, T. / Sweet, R. / Snyder, L. / Gilliland, G.
CitationJournal: Mol.Immunol. / Year: 2012
Title: Structural basis for high selectivity of anti-CCL2 neutralizing antibody CNTO 888.
Authors: Obmolova, G. / Teplyakov, A. / Malia, T.J. / Grygiel, T.L. / Sweet, R. / Snyder, L.A. / Gilliland, G.L.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: CNTO888 LIGHT CHAIN
H: CNTO888 HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,3172
Polymers47,3172
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-26 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.540, 121.540, 84.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Antibody CNTO888 LIGHT CHAIN


Mass: 23625.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): (HEK) 293 / Production host: HOMO SAPIENS (human)
#2: Antibody CNTO888 HEAVY CHAIN


Mass: 23691.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): (HEK) 293 / Production host: HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.17 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4.3 M SODIUM FORMATE CRYO VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 16, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 18826 / Num. obs: 18826 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.455 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.69 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.286 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24912 965 5 %RANDOM
Rwork0.19057 ---
all0.19364 17765 --
obs0.19364 17765 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---1.21 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 130 3338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223286
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9544475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63824.331127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48815513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6481512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2507
X-RAY DIFFRACTIONr_gen_planes_refined00.0212476
X-RAY DIFFRACTIONr_mcbond_it2.7622111
X-RAY DIFFRACTIONr_mcangle_it5.31843409
X-RAY DIFFRACTIONr_scbond_it44.528881175
X-RAY DIFFRACTIONr_scangle_it39.058881066
LS refinement shellResolution: 2.606→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 60 -
Rwork0.314 1272 -
obs--98.4 %

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