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- PDB-5doo: The structure of PKMT2 from Rickettsia typhi -

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Basic information

Entry
Database: PDB / ID: 5doo
TitleThe structure of PKMT2 from Rickettsia typhi
Componentsprotein lysine methyltransferase 2
KeywordsTRANSFERASE / methyltransferase / rossman fold / sam binding protein / methylation
Function / homologyMethyltransferase regulatory domain, predicted / Predicted methyltransferase regulatory domain / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / metal ion binding / Methyltransferase
Function and homology information
Biological speciesRickettsia typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.133 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 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)122,8854
Polymers122,8042
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-37 kcal/mol
Surface area46850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.719, 90.528, 106.201
Angle α, β, γ (deg.)90.000, 114.170, 90.000
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.98 Å3/Da / Density % sol: 58.71 %
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: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / % possible obs: 95.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 73.37 Å2 / Rsym value: 0.112 / Χ2: 1.697 / Net I/av σ(I): 15.121 / Net I/σ(I): 6.4 / Num. measured all: 183801
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.213.60.76949891.07796
3.21-3.343.60.56549741.11195.9
3.34-3.493.60.42850071.20996.6
3.49-3.683.50.35149471.33895.2
3.68-3.913.60.25950281.49196.2
3.91-4.213.60.19349931.74695.4
4.21-4.633.60.1349662.08895.6
4.63-5.33.70.1149712.15695
5.3-6.673.90.10451001.98896.1
6.67-5040.0551302.54594.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 5DO0

5do0


Resolution: 3.133→48.447 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2803 1244 5.03 %
Rwork0.233 23479 -
obs0.2353 24723 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.58 Å2 / Biso mean: 78.9231 Å2 / Biso min: 24.21 Å2
Refinement stepCycle: final / Resolution: 3.133→48.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8165 0 2 0 8167
Biso mean--71.59 --
Num. residues----1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058346
X-RAY DIFFRACTIONf_angle_d0.98311325
X-RAY DIFFRACTIONf_chiral_restr0.0491298
X-RAY DIFFRACTIONf_plane_restr0.0061438
X-RAY DIFFRACTIONf_dihedral_angle_d18.3165014
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1329-3.25840.37381090.35721979208874
3.2584-3.40660.41220.34092664278698
3.4066-3.58620.3831540.30762641279599
3.5862-3.81080.33931260.27162704283099
3.8108-4.10490.28551660.23422656282299
4.1049-4.51770.25381350.20012673280899
4.5177-5.17070.23891580.19312687284599
5.1707-6.51210.28041370.23427292866100
6.5121-48.45230.22261370.18852746288399
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)
1-0.09820.3561-0.07260.5104-0.32250.68290.1441-0.01830.10870.4913-0.0837-0.3306-0.05480.0802-0.00050.3090.0493-0.04080.3626-0.02110.4673-43.6975-7.957331.2717
20.4031-0.0521-0.39310.24960.38890.9654-0.0460.0604-0.0545-0.0178-0.0091-0.20170.0673-0.0711-0.00460.45390.02130.02890.3191-0.02120.3139-57.033-14.142715.3909
30.7968-0.40710.88390.40220.34320.2248-0.0222-0.03080.05220.13560.07370.00250.0922-0.13240.00010.34960.01710.04820.31880.00860.2692-72.2257-3.476238.9293
40.5021-0.3203-0.14220.03060.26371.0464-0.07620.0049-0.04060.04550.1028-0.07470.0170.1757-00.4401-0.0293-0.02450.4325-0.01740.4466-50.7544-15.6795-19.3089
50.50370.05280.33730.0333-0.54141.1756-0.4167-0.20460.1687-0.03380.257-0.1102-0.6451-0.5206-0.30440.5770.1457-0.13260.43890.01950.6351-72.9218-0.4995-27.6333
60.61890.4379-0.12790.3884-0.41830.3507-0.1513-0.0096-0.1674-0.27170.1548-0.1422-0.11760.0398-00.3683-0.0652-0.02030.39930.00240.4895-69.9378-27.3068-37.4879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 138 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 319 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 534 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 252 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 253 through 400 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 401 through 534 )B0

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