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- PDB-1p0y: Crystal structure of the SET domain of LSMT bound to MeLysine and... -

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Basic information

Entry
Database: PDB / ID: 1p0y
TitleCrystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy
ComponentsRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
KeywordsTRANSFERASE / SET DOMAIN / LYSINE N-METHYLATION / MULTIPLE METHYLATION / PHOTOSYNTHESIS / POST-TRANSLATIONAL MODIFICATION
Function / homology
Function and homology information


[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase / [fructose-bisphosphate aldolase]-lysine N-methyltransferase / [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity / protein-lysine N-methyltransferase activity / chloroplast / methylation
Similarity search - Function
Rubisco LSMT methyltransferase, plant / RBCMT, SET domain / Plant LSMT protein-lysine methyltransferase family profile. / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : ...Rubisco LSMT methyltransferase, plant / RBCMT, SET domain / Plant LSMT protein-lysine methyltransferase family profile. / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-METHYL-LYSINE / S-ADENOSYL-L-HOMOCYSTEINE / Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTrievel, R.C. / Flynn, E.M. / Houtz, R.L. / Hurley, J.H.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT
Authors: Trievel, R.C. / Flynn, E.M. / Houtz, R.L. / Hurley, J.H.
History
DepositionApr 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE AUTHORS INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE ...SEQUENCE AUTHORS INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE THAT WAS ENGINEERED INTO THE ENZYME AFTER LEU 482. AFTER CLEAVAGE, THESE SIX RESIDUES WERE LEFT ON THE C-TERMINUS OF THIS CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
B: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
C: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,5219
Polymers151,8873
Non-polymers1,6346
Water11,746652
1
A: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0142
Polymers50,6291
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0142
Polymers50,6291
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast
hetero molecules


  • defined by author
  • 51.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)51,4945
Polymers50,6291
Non-polymers8654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.410, 153.190, 266.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplast / [Ribulose-bisphosphate-carboxylase]-lysine N-methyltransferase / RuBisCO methyltransferase / ...[Ribulose-bisphosphate-carboxylase]-lysine N-methyltransferase / RuBisCO methyltransferase / RuBisco LSMT / rbcMT


Mass: 50629.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q43088, [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-MLZ / N-METHYL-LYSINE


Type: L-peptide linking / Mass: 160.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 4.2 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.95-1.10 M Sodium Acetate, 100 mM Methyllysine Acetate, 1 mM TCEP, 400 uM S-adenosylhomocysteine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.95-1.10 Msodium acetate1reservoir
34000 nMAdoHcy1reservoir
41 mMTCEP1reservoir
5100 mMLys1reservoiror MeLys, pH6.8

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 25, 2003 / Details: Osmic Confocal Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 84637 / Num. obs: 83829 / % possible obs: 96.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.044 / Net I/σ(I): 30.2
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 2.45 / Num. unique all: 7768 / Rsym value: 0.485 / % possible all: 93.6
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 93.6 % / Num. unique obs: 7768 / Rmerge(I) obs: 0.485

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MLV

1mlv


Resolution: 2.55→29.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 935740.33 / Data cutoff high rms absF: 935740.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3761 5.1 %RANDOM
Rwork0.228 ---
all0.23 83829 --
obs0.228 74004 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0102 Å2 / ksol: 0.345424 e/Å3
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1--26.08 Å20 Å20 Å2
2--35 Å20 Å2
3----8.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 2.55→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10545 0 111 652 11308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.692.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.443 536 5.3 %
Rwork0.42 9557 -
obs--70.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAH.PARSAH.TOP
X-RAY DIFFRACTION4MLZ.PARMLZ.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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