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- PDB-6ldv: Structure antibody F9 in complex with methylated peptide -

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Basic information

Entry
Database: PDB / ID: 6ldv
TitleStructure antibody F9 in complex with methylated peptide
Components
  • Fab heavy chain
  • Fab light chain
  • GLY-M3L-GLY-GLY-THR-TYR-PRO
KeywordsIMMUNE SYSTEM / methylation / antibody / phage display / biomolecular recognition
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / cellular response to mechanical stimulus / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding ...mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / cellular response to mechanical stimulus / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Mitogen-activated protein kinase kinase kinase 2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCaaveiro, J.M.M. / Tsumoto, K.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for antigen recognition by methylated lysine-specific antibodies.
Authors: Ishii, M. / Nakakido, M. / Caaveiro, J.M.M. / Kuroda, D. / Okumura, C.J. / Maruyama, T. / Entzminger, K. / Tsumoto, K.
History
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
P: GLY-M3L-GLY-GLY-THR-TYR-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,44811
Polymers52,4333
Non-polymers1,0158
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-36 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.764, 63.526, 125.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-454-

HOH

21H-530-

HOH

31H-542-

HOH

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Components

#1: Antibody Fab heavy chain


Mass: 25532.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): 293 / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 25301.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell (production host): 293 / Production host: Homo sapiens (human)
#3: Protein/peptide GLY-M3L-GLY-GLY-THR-TYR-PRO


Mass: 1598.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2U5*PLUS
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium iodide 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Aug 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.32 Å / Num. obs: 31867 / % possible obs: 99.2 % / Redundancy: 14.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.052 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1856 / CC1/2: 0.677 / Rpim(I) all: 0.379

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M63

5m63


Resolution: 1.9→46.32 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.033 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 1293 4.1 %RANDOM
Rwork0.1794 ---
obs0.1814 30528 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.35 Å2 / Biso mean: 19.912 Å2 / Biso min: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.41 Å2
Refinement stepCycle: final / Resolution: 1.9→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3138 0 11 378 3527
Biso mean--37.04 25.35 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172873
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6584452
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5636708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32723.175126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53115465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911511
X-RAY DIFFRACTIONr_chiral_restr0.0690.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023641
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
LS refinement shellResolution: 1.902→1.951 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 95 -
Rwork0.26 1960 -
all-2055 -
obs--89 %

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