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- PDB-6ldw: Structure of antibody C9 in complex with methylated peptide -

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Basic information

Entry
Database: PDB / ID: 6ldw
TitleStructure of antibody C9 in complex with methylated peptide
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY
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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm ...mitogen-activated protein kinase kinase kinase / MAP kinase kinase kinase activity / cellular response to mechanical stimulus / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
A: Fab light chain
B: Fab heavy chain
D: ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY
C: ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2939
Polymers104,2006
Non-polymers943
Water12,412689
1
L: Fab light chain
H: Fab heavy chain
C: ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1354
Polymers52,1003
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-52 kcal/mol
Surface area18560 Å2
MethodPISA
2
A: Fab light chain
B: Fab heavy chain
D: ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1585
Polymers52,1003
Non-polymers582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-56 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.310, 75.680, 76.320
Angle α, β, γ (deg.)73.980, 87.160, 84.780
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLA2 - 2132 - 213
21ASPASPAC2 - 2132 - 213
12SERSERHB1 - 2101 - 210
22SERSERBD1 - 2101 - 210

NCS ensembles :
ID
1
2

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Components

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Protein/peptide , 1 types, 2 molecules DC

#3: Protein/peptide ILE-PHE-GLU-LYS-PHE-GLY-M3L-GLY-GLY


Mass: 1598.839 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y2U5*PLUS

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 25283.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 25217.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 692 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.86 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium chloride hexahydrate, 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: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45.7 Å / Num. obs: 106948 / % possible obs: 96.3 % / Redundancy: 2 % / R split: 0.04 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.4
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 15357 / Rpim(I) all: 0.346

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LDV

6ldv


Resolution: 1.6→39.16 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.602 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 3283 3.1 %RANDOM
Rwork0.1712 ---
obs0.1732 103662 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 107.26 Å2 / Biso mean: 27.506 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0.26 Å21.38 Å2
2---0.83 Å20.69 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.6→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6211 0 3 691 6905
Biso mean--32.07 33.65 -
Num. residues----837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175708
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6568800
X-RAY DIFFRACTIONr_angle_other_deg1.3631.56313327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7115843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08223.671237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09315926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6631516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021261
X-RAY DIFFRACTIONr_rigid_bond_restr2.88312117
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L62580.08
12A62580.08
21H58070.06
22B58070.06
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 240 -
Rwork0.294 7550 -
all-7790 -
obs--94.54 %

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