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- PDB-4yhy: Crystal structure of 309M3-B in complex with trimethylated Lys -

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Basic information

Entry
Database: PDB / ID: 4yhy
TitleCrystal structure of 309M3-B in complex with trimethylated Lys
Components
  • Fab Heavy Chain
  • Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Trimethylated Lys
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / N-TRIMETHYLLYSINE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHattori, T. / Dementieva, I.S. / Montano, S.P. / Koide, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R21 DA025725 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)RC1 DA028779 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.
Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / ...Authors: Hattori, T. / Lai, D. / Dementieva, I.S. / Montano, S.P. / Kurosawa, K. / Zheng, Y. / Akin, L.R. / Swist-Rosowska, K.M. / Grzybowski, A.T. / Koide, A. / Krajewski, K. / Strahl, B.D. / Kelleher, N.L. / Ruthenburg, A.J. / Koide, S.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
C: Fab Light Chain
B: Fab Heavy Chain
H: Fab Heavy Chain
L: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2596
Polymers95,8814
Non-polymers3792
Water10,881604
1
C: Fab Light Chain
B: Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1303
Polymers47,9402
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-24 kcal/mol
Surface area19520 Å2
MethodPISA
2
H: Fab Heavy Chain
L: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1303
Polymers47,9402
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-25 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.979, 100.342, 135.287
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 Fab Light Chain


Mass: 23269.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC 55244
#2: Antibody Fab Heavy Chain


Mass: 24670.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): ATCC 55244
#3: Chemical ChemComp-M3L / N-TRIMETHYLLYSINE


Type: L-peptide linking / Mass: 189.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H21N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% PEG 3350, 10% Tacsimate (pH7.0), 10 mM EDTA, 1% MPD, 10 mM Sarcosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 79791 / % possible obs: 98.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.5 / % possible all: 84.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R8S, 2DD8, 1MHP

2r8s

2dd8

1mhp


Resolution: 1.9→39.848 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 3995 5.02 %
Rwork0.206 --
obs0.2078 79566 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→39.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6498 0 26 604 7128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076686
X-RAY DIFFRACTIONf_angle_d1.0619108
X-RAY DIFFRACTIONf_dihedral_angle_d12.6132360
X-RAY DIFFRACTIONf_chiral_restr0.0411026
X-RAY DIFFRACTIONf_plane_restr0.0051172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.92280.30841320.28692012X-RAY DIFFRACTION77
1.9228-1.94630.28861100.28062353X-RAY DIFFRACTION91
1.9463-1.97090.29781050.27522549X-RAY DIFFRACTION96
1.9709-1.99680.2991350.25192518X-RAY DIFFRACTION97
1.9968-2.02420.27561470.24192575X-RAY DIFFRACTION97
2.0242-2.05310.27941240.23432593X-RAY DIFFRACTION98
2.0531-2.08370.25941280.21912622X-RAY DIFFRACTION99
2.0837-2.11630.24421430.20142571X-RAY DIFFRACTION99
2.1163-2.1510.25141470.21952613X-RAY DIFFRACTION100
2.151-2.18810.27011480.20922618X-RAY DIFFRACTION100
2.1881-2.22790.27621250.21382629X-RAY DIFFRACTION99
2.2279-2.27070.24281350.21332617X-RAY DIFFRACTION100
2.2707-2.31710.26461370.21422602X-RAY DIFFRACTION100
2.3171-2.36740.24581400.21092638X-RAY DIFFRACTION100
2.3674-2.42250.27771260.21632641X-RAY DIFFRACTION100
2.4225-2.48310.30781370.2262623X-RAY DIFFRACTION100
2.4831-2.55020.27671400.22222634X-RAY DIFFRACTION100
2.5502-2.62520.25541620.22032613X-RAY DIFFRACTION100
2.6252-2.70990.22161300.21232663X-RAY DIFFRACTION100
2.7099-2.80680.28571450.22142628X-RAY DIFFRACTION100
2.8068-2.91910.21941420.21592654X-RAY DIFFRACTION100
2.9191-3.05190.25731360.222664X-RAY DIFFRACTION100
3.0519-3.21280.25541390.22162655X-RAY DIFFRACTION100
3.2128-3.4140.26251380.21312668X-RAY DIFFRACTION100
3.414-3.67740.25571490.19622676X-RAY DIFFRACTION100
3.6774-4.04710.20511610.19062658X-RAY DIFFRACTION100
4.0471-4.6320.1771510.15692700X-RAY DIFFRACTION100
4.632-5.83290.20831370.16422746X-RAY DIFFRACTION100
5.8329-39.85630.20581460.19392838X-RAY DIFFRACTION99

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