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- PDB-3tr6: Structure of a O-methyltransferase from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tr6
TitleStructure of a O-methyltransferase from Coxiella burnetii
ComponentsO-methyltransferase
KeywordsTRANSFERASE / Cellular processes
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
: / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _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.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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8463
Polymers25,4031
Non-polymers4432
Water1,820101
1
A: O-methyltransferase
hetero molecules

A: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6936
Polymers50,8072
Non-polymers8864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area5740 Å2
ΔGint-60 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.686, 83.686, 212.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

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Components

#1: Protein O-methyltransferase


Mass: 25403.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0924 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83D22, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.24 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.01M Nickel (II) chloride, 20% PEG MME 2000, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 13010 / Num. obs: 12763 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.074 / Χ2: 1.08 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.756.40.275660.47191.1
2.75-2.87.10.2645890.525193
2.8-2.858.10.2515810.524193.7
2.85-2.9190.2326070.548195.6
2.91-2.9710.50.226040.517195.6
2.97-3.0412.60.216150.533197.6
3.04-3.1213.50.1926260.602198
3.12-3.213.50.156050.665197.9
3.2-3.2913.30.1376260.768198.9
3.29-3.413.30.1176450.864199.2
3.4-3.5213.30.1016490.981199.8
3.52-3.6613.80.0956331.1421100
3.66-3.83140.0846581.3131100
3.83-4.0314.80.086371.3661100
4.03-4.28150.0686581.5241100
4.28-4.6115.90.0646501.6511100
4.61-5.0716.20.0586651.6311100
5.07-5.817.20.0586791.2451100
5.8-7.317.20.0536971.1081100
7.3-3015.70.047731.545199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.845 Å / Occupancy max: 1 / Occupancy min: 0.81 / FOM work R set: 0.8477 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 614 4.84 %RANDOM
Rwork0.2016 ---
all0.2037 13628 --
obs0.2037 12694 97.65 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.342 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 124.68 Å2 / Biso mean: 41.5431 Å2 / Biso min: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.0558 Å20 Å20 Å2
2---3.0558 Å20 Å2
3---6.1115 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 27 101 1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031800
X-RAY DIFFRACTIONf_angle_d0.8142439
X-RAY DIFFRACTIONf_chiral_restr0.056288
X-RAY DIFFRACTIONf_plane_restr0.002308
X-RAY DIFFRACTIONf_dihedral_angle_d14.27678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.95780.36061620.26522748291092
2.9578-3.38530.2751670.22022957312498
3.3853-4.26320.21971370.187830873224100
4.2632-29.8450.22141480.187232883436100

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