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- PDB-5do0: The structure of PKMT1 from Rickettsia prowazekii -

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Basic information

Entry
Database: PDB / ID: 5do0
TitleThe structure of PKMT1 from Rickettsia prowazekii
Componentsprotein lysine methyltransferase 1
KeywordsTRANSFERASE / methyltransferase / rossman fold / sam binding protein / methylation
Function / homologyMethyltransferase regulatory domain, predicted / : / Predicted methyltransferase regulatory domain / PKMT, C-terminal winged helix domain / : / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Uncharacterized protein RP789
Function and homology information
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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

Downloads & links

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Assembly

Deposited unit
B: protein lysine methyltransferase 1
A: protein lysine methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)126,9682
Polymers126,9682
Non-polymers00
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-18 kcal/mol
Surface area46150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.498, 62.466, 107.853
Angle α, β, γ (deg.)90.000, 100.780, 90.000
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES-NaOH buffer at pH 7.5, 10 % v/v isopropanol, 20 % w/v polyethylene glycol 4000

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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: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 40220 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rsym value: 0.163 / Χ2: 1.375 / Net I/av σ(I): 9.523 / Net I/σ(I): 5.4 / Num. measured all: 148342
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.692.90.68538381.34796.9
2.69-2.83.50.62240181.13699.7
2.8-2.933.60.48340001.05699.9
2.93-3.083.70.38340311.028100
3.08-3.283.80.27440151.02100
3.28-3.533.90.19140271.199100
3.53-3.883.90.1540571.383100
3.88-4.453.90.11240381.71499.9
4.45-5.63.90.09540571.90699.7
5.6-503.70.06541391.87198.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.6→48.379 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 2000 4.98 %
Rwork0.2136 38193 -
obs0.2151 40193 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.35 Å2 / Biso mean: 45.4265 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: final / Resolution: 2.6→48.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8012 0 0 333 8345
Biso mean---34.68 -
Num. residues----1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048175
X-RAY DIFFRACTIONf_angle_d0.85611089
X-RAY DIFFRACTIONf_chiral_restr0.051271
X-RAY DIFFRACTIONf_plane_restr0.0041430
X-RAY DIFFRACTIONf_dihedral_angle_d17.264956
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 (%)
2.5872-2.65190.33561270.31712432255989
2.6519-2.72350.35871420.30442695283799
2.7235-2.80370.30321430.281227412884100
2.8037-2.89420.3351440.259927362880100
2.8942-2.99760.29581430.26227512894100
2.9976-3.11760.28951440.24827432887100
3.1176-3.25940.29141420.241427042846100
3.2594-3.43120.23611440.22427612905100
3.4312-3.64620.25121440.213727562900100
3.6462-3.92760.23841440.188827462890100
3.9276-4.32260.19361450.176827742919100
4.3226-4.94750.18131440.164127462890100
4.9475-6.23130.20291460.200327912937100
6.2313-48.38780.20231480.17882817296598
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)
11.82180.00560.08950.879-0.46322.8787-0.0804-0.04560.24820.2004-0.09680.0423-0.3510.05010.17410.23290.00640.01120.21610.01950.240321.196112.1481-84.0483
22.4970.6980.68751.53830.91923.9486-0.0245-0.2207-0.14720.1075-0.0727-0.08290.08620.13130.06590.27280.00870.01280.34930.07910.236524.7839-2.2326-77.2383
35.92191.25190.9785.86150.29873.8916-0.17380.35390.18450.0420.1289-0.9347-0.29530.3623-0.01680.26750.00480.03180.2707-0.00180.284351-1.629-95.2177
41.8283-0.5611-0.26852.78140.03630.854-0.03050.42740.2466-0.15780.046-0.3222-0.08330.10030.00920.1794-0.0084-0.01140.46760.07210.310743.299412.2521-102.2773
52.31070.48790.39611.857-1.27992.8505-0.0449-0.2608-0.0368-0.0143-0.07890.17610.077-0.62140.04460.248-0.01920.01070.3927-0.0990.291419.69975.892-30.844
61.6902-2.2019-2.30354.95684.44136.6461-0.1846-0.213-0.10810.01130.3099-0.14230.47890.6551-0.16490.3058-0.0042-0.07230.44570.03650.285929.843-1.2184-55.7158
73.64350.1075-0.17623.52320.87065.6564-0.01880.20870.2912-0.3339-0.09180.0823-0.420.02660.13360.29250.019-0.07590.38180.02710.210327.903116.7442-47.1888
82.94361.33050.46752.07430.58091.9132-0.0063-0.0196-0.67660.16510.0495-0.58560.16680.24030.010.2631-0.0022-0.0690.36330.00530.457648.10411.527-26.5054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 43 through 242 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 243 through 336 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 337 through 377 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 378 through 553 )B0
5X-RAY DIFFRACTION5chain 'A' and (resid 43 through 166 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 167 through 242 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 243 through 336 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 337 through 553 )A0

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