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- PDB-4k7p: Generation and Characterization of a Unique Reagent that Recogniz... -

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Basic information

Entry
Database: PDB / ID: 4k7p
TitleGeneration and Characterization of a Unique Reagent that Recognizes a Panel of Recombinant Human Monoclonal Antibody Therapeutics in the Presence of Endogenous Human IgG
Components
  • antibody 10C4 Fab fragment heavy chain
  • antibody 10C4 Fab fragment light chain
  • antibody rhumAb6 Fab fragment heavy chain
  • antibody rhumAb6 Fab fragment light chain
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsEigenbrot, C. / Shia, S.
CitationJournal: MAbs / Year: 2013
Title: Generation and characterization of a unique reagent that recognizes a panel of recombinant human monoclonal antibody therapeutics in the presence of endogenous human IgG.
Authors: Wang, X. / Quarmby, V. / Ng, C. / Chuntharapai, A. / Shek, T. / Eigenbrot, C. / Kelley, R.F. / Shia, S. / McCutcheon, K. / Lowe, J. / Leddy, C. / Coachman, K. / Cain, G. / Chu, F. / Hotzel, ...Authors: Wang, X. / Quarmby, V. / Ng, C. / Chuntharapai, A. / Shek, T. / Eigenbrot, C. / Kelley, R.F. / Shia, S. / McCutcheon, K. / Lowe, J. / Leddy, C. / Coachman, K. / Cain, G. / Chu, F. / Hotzel, I. / Maia, M. / Wakshull, E. / Yang, J.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: antibody rhumAb6 Fab fragment light chain
Y: antibody rhumAb6 Fab fragment heavy chain
H: antibody 10C4 Fab fragment heavy chain
L: antibody 10C4 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)95,6524
Polymers95,6524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-59 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.917, 109.099, 119.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody antibody rhumAb6 Fab fragment light chain


Mass: 23225.752 Da / Num. of mol.: 1 / Fragment: Fab rhumAb6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody antibody rhumAb6 Fab fragment heavy chain


Mass: 24643.645 Da / Num. of mol.: 1 / Fragment: Fab 10C4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody antibody 10C4 Fab fragment heavy chain


Mass: 24308.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody antibody 10C4 Fab fragment light chain


Mass: 23474.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM NaCl, phosphate buffer, PEG1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 25878 / Num. obs: 25377 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.179 / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVD

1fvd


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.855 / SU B: 43.673 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28402 1046 4.1 %RANDOM
Rwork0.21923 ---
obs0.22184 24331 99.12 %-
all-25878 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.431 Å2
Baniso -1Baniso -2Baniso -3
1-5.96 Å2-0 Å2-0 Å2
2---2.25 Å2-0 Å2
3----3.71 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 0 0 6560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026734
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9479173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0745853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29924.701268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.059151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1711518
X-RAY DIFFRACTIONr_chiral_restr0.0650.21017
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215103
LS refinement shellResolution: 2.95→3.109 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.368 114 -
Rwork0.309 3109 -
obs--94.74 %
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)
10.3247-0.29580.47490.3444-0.77273.1258-0.05530.01340.04220.04370.0967-0.0786-0.1516-0.4783-0.04140.21370.05760.00630.2332-0.03240.138-25.25737.347929.5424
23.1329-1.60820.58781.8836-1.59771.7771-0.5434-0.39450.22680.26850.3913-0.1966-0.2824-0.43990.15210.50670.312-0.1310.2505-0.11360.0584-44.890931.288613.8944
30.14810.2850.08550.8417-0.41931.5963-0.0214-0.0318-0.0804-0.004-0.0574-0.1122-0.10130.0390.07890.1810.0799-0.01350.15660.00660.1756-4.3799-4.84149.631
40.2760.6866-0.30092.5112-0.07181.1962-0.08260.0126-0.07570.02170.188-0.29050.04240.283-0.10550.1781-0.01980.05410.1595-0.01960.216514.174210.273825.7343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 113
2X-RAY DIFFRACTION1L1 - 108
3X-RAY DIFFRACTION2H114 - 211
4X-RAY DIFFRACTION2L109 - 214
5X-RAY DIFFRACTION3Y1 - 115
6X-RAY DIFFRACTION3X1 - 109
7X-RAY DIFFRACTION4Y116 - 214
8X-RAY DIFFRACTION4X110 - 214

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