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

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Basic information

Entry
Database: PDB / ID: 5dnk
TitleThe structure of PKMT1 from Rickettsia prowazekii in complex with AdoHcy
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-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein RP789
Function and homology information
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 10, 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)127,7374
Polymers126,9682
Non-polymers7692
Water16,718928
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-21 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.016, 62.127, 107.392
Angle α, β, γ (deg.)90.00, 100.88, 90.00
Int Tables number4
Space group name H-MP1211

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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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, pH 8.5, 20 % w/v polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 134251 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rsym value: 0.12 / Χ2: 1.606 / Net I/av σ(I): 13.9 / Net I/σ(I): 5.2 / Num. measured all: 429501
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.972.80.721.5117391.0997.3
2.18-2.263.20.689120141.15781.3
2.26-2.373.20.57122971.16683.1
2.37-2.493.10.433126671.20485.7
2.49-2.653.10.333131351.34388.6
2.65-2.853.10.234136871.48792.3
2.85-3.143.10.163141841.63795.4
3.14-3.593.20.112145102.03897.5
3.59-4.523.30.082147852.33298.7
4.52-503.50.065152332.09399.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142)refinement
Blu-IceJBluIcedata collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.998 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1999 2.01 %
Rwork0.2024 --
obs0.2034 99427 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 52 928 9024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078274
X-RAY DIFFRACTIONf_angle_d1.03711229
X-RAY DIFFRACTIONf_dihedral_angle_d19.0885005
X-RAY DIFFRACTIONf_chiral_restr0.0681279
X-RAY DIFFRACTIONf_plane_restr0.0081446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.94730.34141330.31976508X-RAY DIFFRACTION93
1.9473-1.99990.36171430.29156933X-RAY DIFFRACTION99
1.9999-2.05870.28281410.26256871X-RAY DIFFRACTION99
2.0587-2.12510.28871420.24286959X-RAY DIFFRACTION100
2.1251-2.2010.26761430.22216957X-RAY DIFFRACTION100
2.201-2.2890.2271440.21276992X-RAY DIFFRACTION100
2.289-2.3930.27091430.20826986X-RAY DIFFRACTION100
2.393-2.51890.28861430.2116966X-RAY DIFFRACTION100
2.5189-2.67640.27641430.21086985X-RAY DIFFRACTION100
2.6764-2.88250.26951440.20247025X-RAY DIFFRACTION100
2.8825-3.17150.26861430.20136982X-RAY DIFFRACTION100
3.1715-3.62810.24771440.18497021X-RAY DIFFRACTION100
3.6281-4.5620.18481450.16467042X-RAY DIFFRACTION100
4.562-19.9990.21761480.17737201X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.59850.2644-0.20321.1880.13961.47850.015-0.11080.0741-0.0346-0.0092-0.0709-0.07050.15790.0030.1062-0.01470.01590.0974-0.00830.081642.8314-6.954339.8699
21.3232-0.47330.34480.9607-0.41522.3349-0.06010.15410.018-0.0494-0.02250.088-0.1448-0.36870.04180.16410.0071-0.00560.2186-0.03750.127732.4517-10.65420.9089
31.19540.5696-0.14832.57650.10630.7417-0.0807-0.05980.14520.00750.10470.4177-0.0744-0.1034-0.00590.11420.01570.01110.14030.00860.190214.5155-6.550247.7555
42.0544-0.43610.54491.46840.72231.6315-0.01430.33760.0522-0.1355-0.1037-0.1834-0.07750.39430.10390.16610.02390.02660.30430.06080.144439.1409-10.8589-22.2857
51.19750.26950.41031.6443-1.20233.5187-0.1016-0.07270.08580.0783-0.0728-0.0145-0.19-0.21550.15580.16470.0427-0.01810.2323-0.03420.13430.6564-8.6674-2.0868
62.4064-1.16550.64841.5725-0.29041.9366-0.1371-0.1386-0.4039-0.07360.13420.4810.1789-0.30160.01970.20370.0282-0.01020.28430.03660.305110.805-14.3439-26.3134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 336 )
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 553 )
4X-RAY DIFFRACTION4chain 'B' and (resid 44 through 166 )
5X-RAY DIFFRACTION5chain 'B' and (resid 167 through 336 )
6X-RAY DIFFRACTION6chain 'B' and (resid 337 through 553 )

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