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- PDB-7bg1: Structure of anti-FLAG M2 Fab domain remodeled based on proteomic... -

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Basic information

Entry
Database: PDB / ID: 7bg1
TitleStructure of anti-FLAG M2 Fab domain remodeled based on proteomic sequencing
Components
  • anti-FLAG M2 heavy chain
  • anti-FLAG M2 light chain
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin / IgG / Fab / Monoclonal / M2 / Protein purification / FLAG / anti-FLAG / FLAG-tag / Immunohistochemistry / Immunocytochemistry / Immunoprecipitation / ELISA / Western blot / Research tool / Affinity tag
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsPronker, M.F. / Snijder, J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)024.002.009 Netherlands
Citation
Journal: J.Proteome Res. / Year: 2021
Title: Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme.
Authors: Peng, W. / Pronker, M.F. / Snijder, J.
#1: Journal: Biorxiv / Year: 2021
Title: Mass spectrometry-based de novo sequencing of the anti-FLAG-M2 antibody using multiple proteases and a dual fragmentation scheme
Authors: Peng, W. / Pronker, M.F. / Snijder, J.
History
DepositionJan 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
H: anti-FLAG M2 heavy chain
L: anti-FLAG M2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4995
Polymers48,2722
Non-polymers2283
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Standard Fab
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-50 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.360, 133.760, 41.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Antibody anti-FLAG M2 heavy chain


Mass: 23907.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IGHV1-04/IGHJ2 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): Ovarian
#2: Antibody anti-FLAG M2 light chain


Mass: 24364.111 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) / Tissue (production host): Ovarian
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 4000, 0.1M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 46087 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Biso Wilson estimate: 30.69 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.249 / Num. unique obs: 2659 / % possible all: 58.9

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Processing

Software
NameVersionClassification
Coot1.17.1_3660model building
PHENIX1.17.1_3660refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G60

2g60


Resolution: 1.86→41.52 Å / SU ML: 0.2045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2552 2008 5.02 %
Rwork0.2173 37980 -
obs0.2192 39988 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.35 Å2
Refinement stepCycle: LAST / Resolution: 1.86→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 11 250 3497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353327
X-RAY DIFFRACTIONf_angle_d0.72654534
X-RAY DIFFRACTIONf_chiral_restr0.0488506
X-RAY DIFFRACTIONf_plane_restr0.0039574
X-RAY DIFFRACTIONf_dihedral_angle_d18.93051184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.29921220.27411967X-RAY DIFFRACTION71.96
1.91-1.960.28831210.25172254X-RAY DIFFRACTION80.89
1.96-2.020.26831240.26232546X-RAY DIFFRACTION90.79
2.02-2.080.2981370.25392793X-RAY DIFFRACTION98.89
2.08-2.160.32341590.25052776X-RAY DIFFRACTION99.69
2.16-2.240.29121420.24012797X-RAY DIFFRACTION100
2.24-2.340.25681640.23682780X-RAY DIFFRACTION100
2.34-2.470.27361470.24562831X-RAY DIFFRACTION100
2.47-2.620.29431560.2392814X-RAY DIFFRACTION100
2.62-2.820.24971360.23342824X-RAY DIFFRACTION100
2.82-3.110.29631300.22922878X-RAY DIFFRACTION100
3.11-3.560.2831630.20872847X-RAY DIFFRACTION99.97
3.56-4.480.20771720.18472874X-RAY DIFFRACTION99.67
4.48-41.520.21931350.19942999X-RAY DIFFRACTION97.45
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)
17.605422889530.801231496795-0.1049569179713.27868782638-0.09019136206621.926337105520.03402862340250.301256082210.214226876907-0.172348220197-0.09337245907050.271044072654-0.145212734805-0.1902040772040.06281888233720.177411700790.0389006158269-0.005237123793270.274157676745-0.05295378047240.24271459361622.805889615832.1660648665-3.8256920579
20.414092649671-0.7103096246781.178464920093.3744888895-1.695872651542.916569332760.388930900203-1.98804462899-0.7864482059690.831307970675-0.2005164517580.584834178490.312690670997-1.00174438618-0.5435252781320.73712498974-0.28130308827-0.02417438236771.368286131450.5852106968130.7403349223817.5746955773.3668871162317.9271767149
35.63425180439-1.215896253025.703578537946.66239158615-0.2655630026855.919029920340.373215903772-0.777817870876-0.02046407360560.353277774115-0.259352946388-0.4808015386930.1019670814050.14831243102-0.112181894780.836277692139-0.572017364222-0.2223993432381.689040102340.3133203409931.4754473760816.3638097606-9.0510995416422.1761952253
44.09373910215-0.05452628330792.324535557820.834324746581-2.619745550068.933941568930.0380784874171-0.285445512586-0.0893769721421-0.0284989696521-0.0255496157295-0.001221162486971.221995285910.112524357166-0.06250718402940.3540216665270.043947722360.01604642657450.336564302319-0.06703686824510.22214854576846.410653017920.27402621522.88074579116
55.221716711110.6281547991150.3453558893833.933860260620.03593748877521.580616418570.0784279817716-0.3173408347680.5528997276380.102442382803-0.022885342640.0856570303523-0.178590469606-0.0342586661859-0.07959172772630.139143192739-0.0106125590351-0.01662645637010.257190064912-0.03666446531160.21681865055242.991774441432.81870481350.199128003731
61.905782621591.710695088630.2460463602993.20182061089-3.109723763166.485516262340.154427484693-0.4325419078760.3457382441370.241942599010.185346579435-0.239010972827-0.3116341674470.597216962899-0.3309620623670.1587740550230.0194222044906-0.0389804241970.342473229663-0.06508716458940.20920223778649.306082687928.08599032095.43743348966
75.988294164750.1158915957770.2839862326495.406287562471.277555970256.808700558060.1355140355360.4582719525840.429473076724-0.518320286893-0.1198722275320.167733305979-0.069763296512-0.391666620062-0.04919828515740.1394963952830.01013431295740.007007636174360.2749563158240.001244442287920.17564234215538.084208881527.3901472747-4.97011895388
84.10534209948-0.09546707418451.173108516314.01966527547-1.589044693842.118960247480.407088202424-0.348154585577-0.797373826191-0.5488770144190.2185938243330.7055553162960.897064893378-0.383191615937-0.3886957494790.569674060597-0.0719774197972-0.158119089970.2875849816980.1207244503280.43486715055531.73737026873.028795317198.61914095587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 118 )
2X-RAY DIFFRACTION2chain 'L' and (resid 119 through 213 )
3X-RAY DIFFRACTION3chain 'L' and (resid 214 through 215 )
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 25 )
5X-RAY DIFFRACTION5chain 'H' and (resid 26 through 66 )
6X-RAY DIFFRACTION6chain 'H' and (resid 67 through 90 )
7X-RAY DIFFRACTION7chain 'H' and (resid 91 through 109 )
8X-RAY DIFFRACTION8chain 'H' and (resid 110 through 224 )

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