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- PDB-5dpd: The structure of PKMT1 from Rickettsia prowazekii in complex with... -

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Basic information

Entry
Database: PDB / ID: 5dpd
TitleThe structure of PKMT1 from Rickettsia prowazekii in complex with AdoMet
Componentsprotein lysine methyltransferase 1
KeywordsTRANSFERASE / methyltransferase / rossman fold / sam binding protein / methylation
Function / homology: / PKMT, C-terminal winged helix domain / Methyltransferase regulatory domain, predicted / Predicted methyltransferase regulatory domain / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYLMETHIONINE / Uncharacterized protein RP789
Function and homology information
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 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 1
B: protein lysine methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,7654
Polymers126,9682
Non-polymers7972
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-19 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.033, 62.935, 107.632
Angle α, β, γ (deg.)90.000, 100.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain C
12(chain A and (resseq 43:45 or (resid 46 and (name...
22(chain B and (resseq 43:45 or (resid 46 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain DD1
211chain CC1
112(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 45
122(chain A and (resseq 43:45 or (resid 46 and (name...A46
132(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
142(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
152(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
162(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
172(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
182(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
192(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
1102(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
1112(chain A and (resseq 43:45 or (resid 46 and (name...A43 - 553
212(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 45
222(chain B and (resseq 43:45 or (resid 46 and (name...B46
232(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
242(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
252(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
262(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
272(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
282(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
292(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
2102(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553
2112(chain B and (resseq 43:45 or (resid 46 and (name...B43 - 553

NCS ensembles :
ID
1
2

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Components

#1: Protein protein lysine methyltransferase 1


Mass: 63484.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (strain Madrid E) (bacteria)
Strain: Madrid E / Gene: RP789 / Production host: Escherichia coli (E. coli) / References: UniProt: O05979
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 4 % v/v isopropanol, 0.1 M Bis-Tris propane, pH 9.0, 20% w/v polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 25149 / % possible obs: 95 % / Redundancy: 2.4 % / Rsym value: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.5 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementResolution: 3→48.207 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2000 7.95 %
Rwork0.1965 23148 -
obs0.1996 25148 94.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.42 Å2 / Biso mean: 60.7299 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 3→48.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8063 0 54 0 8117
Biso mean--61.48 --
Num. residues----1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078295
X-RAY DIFFRACTIONf_angle_d1.24511267
X-RAY DIFFRACTIONf_chiral_restr0.0661289
X-RAY DIFFRACTIONf_plane_restr0.0081452
X-RAY DIFFRACTIONf_dihedral_angle_d19.285011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9858-3.06050.3621250.33371453157886
3.0605-3.14320.3361350.31821556169190
3.1432-3.23570.38241350.2891567170291
3.2357-3.34010.3521400.26631615175593
3.3401-3.45950.2681390.22961620175994
3.4595-3.59790.29241410.21871626176794
3.5979-3.76160.24471450.2121673181895
3.7616-3.95990.26871450.18521677182296
3.9599-4.20780.20311440.17111663180797
4.2078-4.53250.18371470.14381708185598
4.5325-4.98820.18281480.14791715186398
4.9882-5.7090.21851510.17441745189698
5.709-7.18890.24141510.20971737188899
7.1889-48.21360.16431540.16211793194798

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