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- PDB-2h2e: Structure of Rubisco LSMT bound to AzaAdoMet and Lysine -

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Basic information

Entry
Database: PDB / ID: 2h2e
TitleStructure of Rubisco LSMT bound to AzaAdoMet and Lysine
ComponentsRibulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase
KeywordsTRANSFERASE / SET domain / protein lysine methyltransferase
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 substrate-binding ...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 superfamily / SET domain / SET domain profile. / SET domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
LYSINE / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCouture, J.F. / Hauk, G. / Trievel, R.C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Catalytic Roles for Carbon-Oxygen Hydrogen Bonding in SET Domain Lysine Methyltransferases.
Authors: Couture, J.F. / Hauk, G. / Thompson, M.J. / Blackburn, G.M. / Trievel, R.C.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Remark 999The engineered construct possesses an ENLYFQ sequence on its C-terminus due to a TEV protease cleavage site.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,0989
Polymers150,5123
Non-polymers1,5866
Water6,936385
1
A: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6993
Polymers50,1711
Non-polymers5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6993
Polymers50,1711
Non-polymers5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6993
Polymers50,1711
Non-polymers5292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-57 kcal/mol
Surface area59130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.630, 159.490, 267.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThere are three molecules of LSMT in the asymmetric unit. LSMT is a monomer in solution.

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Components

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


Mass: 50170.633 Da / Num. of mol.: 3 / Fragment: Rubisco LSMT (Residues 49-482)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: RBCMT / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: Q43088, [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase
#2: Chemical ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 4.7 Å3/Da / Density % sol: 73.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM NaCitrate pH 6.8, 1.43-1.74 M NaAcetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9686 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 13, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→16.8 Å / Num. all: 87141 / Num. obs: 85610 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 5.5 Å2 / Rsym value: 0.103 / Net I/σ(I): 7.2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→16.73 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 582909.51 / 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
Rfree0.298 4320 5.1 %RANDOM
Rwork0.262 ---
obs0.262 85270 98.2 %-
all-85610 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.878 Å2 / ksol: 0.357042 e/Å3
Displacement parametersBiso mean: 71.5 Å2
Baniso -1Baniso -2Baniso -3
1--11.45 Å20 Å20 Å2
2--16.46 Å20 Å2
3----5.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a1.03 Å0.99 Å
Refinement stepCycle: LAST / Resolution: 2.6→16.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10481 0 111 385 10977
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.682.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.45 740 5.2 %
Rwork0.474 13443 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3aza.paraza.top
X-RAY DIFFRACTION4lys.parlys.top

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