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- PDB-5dpl: The structure of PKMT2 from Rickettsia typhi in complex with AdoHcy -

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Basic information

Entry
Database: PDB / ID: 5dpl
TitleThe structure of PKMT2 from Rickettsia typhi in complex with AdoHcy
Componentsprotein lysine methyltransferase 2
KeywordsTRANSFERASE / methyltransferase / rossman fold / sam binding protein / methylation
Function / homology
Function and homology information


Methyltransferase regulatory domain, predicted / : / Predicted methyltransferase regulatory domain / PKMT, C-terminal winged helix domain / : / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesRickettsia typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNoinaj, N. / Abeykoon, A. / He, Y. / Yang, D.C. / Buchanan, S.K.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Insights into Substrate Recognition and Catalysis in Outer Membrane Protein B (OmpB) by Protein-lysine Methyltransferases from Rickettsia.
Authors: Abeykoon, A.H. / Noinaj, N. / Choi, B.E. / Wise, L. / He, Y. / Chao, C.C. / Wang, G. / Gucek, M. / Ching, W.M. / Chock, P.B. / Buchanan, S.K. / Yang, D.C.
History
DepositionSep 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein lysine methyltransferase 2
B: protein lysine methyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5734
Polymers122,8042
Non-polymers7692
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-33 kcal/mol
Surface area46800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.352, 91.028, 105.827
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein protein lysine methyltransferase 2


Mass: 61402.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia typhi (strain ATCC VR-144 / Wilmington) (bacteria)
Strain: ATCC VR-144 / Wilmington / Gene: RT0101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68XQ5
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.19 M CaCl2, 0.095 M HEPES-NaOH, pH 7.5, 26.6 % polyethylene glycol 400, 5 % v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 23922 / % possible obs: 97.5 % / Redundancy: 2.8 % / Rsym value: 0.14 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.955 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2802 2000 8.36 %
Rwork0.2444 --
obs0.2474 23915 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8010 0 52 0 8062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058264
X-RAY DIFFRACTIONf_angle_d1.16611267
X-RAY DIFFRACTIONf_dihedral_angle_d17.2274918
X-RAY DIFFRACTIONf_chiral_restr0.0581307
X-RAY DIFFRACTIONf_plane_restr0.0061445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1914-3.27120.40621280.37431378X-RAY DIFFRACTION86
3.2712-3.35970.39651410.35171539X-RAY DIFFRACTION97
3.3597-3.45850.36971460.32811534X-RAY DIFFRACTION97
3.4585-3.57010.37981380.3131558X-RAY DIFFRACTION97
3.5701-3.69760.3531430.30221551X-RAY DIFFRACTION97
3.6976-3.84560.31611390.28451570X-RAY DIFFRACTION98
3.8456-4.02060.32321460.26371560X-RAY DIFFRACTION98
4.0206-4.23240.28681450.24221591X-RAY DIFFRACTION99
4.2324-4.49740.24441420.21671584X-RAY DIFFRACTION99
4.4974-4.84440.24351440.20821591X-RAY DIFFRACTION99
4.8444-5.33140.24231460.20541593X-RAY DIFFRACTION99
5.3314-6.10160.30351410.24041603X-RAY DIFFRACTION99
6.1016-7.68260.29581500.24241618X-RAY DIFFRACTION100
7.6826-48.96040.19531510.191645X-RAY DIFFRACTION99

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