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- PDB-3mcz: The Structure of an O-methyltransferase family protein from Burkh... -

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Basic information

Entry
Database: PDB / ID: 3mcz
TitleThe Structure of an O-methyltransferase family protein from Burkholderia thailandensis.
ComponentsO-methyltransferase
KeywordsTRANSFERASE / AdoMet_MTases / S-adenosylmethionine-dependent methyltransferases / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation
Similarity search - Function
Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily ...Acetylserotonin O-methyltransferase, dimerisation domain / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
O-methyltransferase family protein, putative
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of an O-methyltransferase family protein from Burkholderia thailandensis.
Authors: Cuff, M.E. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase
B: O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3084
Polymers78,1232
Non-polymers1842
Water8,125451
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-52 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.252, 136.595, 56.080
Angle α, β, γ (deg.)90.000, 102.550, 90.000
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological assembly is unknown, but possibly the dimer AB in the asymmetric unit.

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Components

#1: Protein O-methyltransferase /


Mass: 39061.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_II1280 / Plasmid: pMCSGB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2T5S3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.9→40.3 Å / Num. all: 47531 / Num. obs: 47531 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 4.8 % / % possible all: 99.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.85 Å / D res low: 50 Å / FOM : 0.239 / FOM acentric: 0.244 / FOM centric: 0 / Reflection: 51428 / Reflection acentric: 50405 / Reflection centric: 1023
Phasing MAD setR cullis acentric: 1.42 / R cullis centric: 1 / Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Loc acentric: 0.2 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 50405 / Reflection centric: 1023
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
11.76-501.330.50.317018
6.66-11.761.260.50.384854
4.65-6.661.370.40.3207581
3.57-4.651.080.30.33849114
2.9-3.571.280.20.16115146
2.44-2.91.660.20.18927170
2.1-2.441.590.10.112305211
1.85-2.11.950.1016116229
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
136.162-0.154-0.989-0.0876.263
240.3298-0.308-0.969-0.2635.679
337.891-0.226-0.459-0.1655.304
438.0576-0.238-0.777-0.3984.174
544.0998-0.653-0.199-0.3174.591
641.1627-0.633-0.196-0.1214.534
744.5361-0.989-0.02-0.1334.213
838.9282-0.422-0.96-0.4043.433
938.6388-0.469-0.229-0.3223.656
1076.4733-0.48-0.262-0.2083.654
1145.1461-0.9-0.516-0.033.414
1252.666-0.41-0.692-0.033.271
1334.7644-0.998-0.976-0.2352.995
1438.2506-0.656-0.179-0.4412.332
1554.3668-0.475-0.248-0.5022.125
1668.3858-0.136-0.529-0.0263.838
1723.65-0.508-0.223-0.4910.754
1846.6035-0.9-0.549-0.0551.925
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
11.76-500.3820.423018817018
6.66-11.760.4640.493090284854
4.65-6.660.4640.48202156207581
3.57-4.650.3940.405039633849114
2.9-3.570.3730.381062616115146
2.44-2.90.3050.311090978927170
2.1-2.440.1940.19801251612305211
1.85-2.10.1040.10501634516116229
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 51428
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.44-10066.60.411509
6.46-8.4459.90.862683
5.43-6.46610.89843
4.77-5.4360.40.911953
4.31-4.7759.50.9211088
3.96-4.3160.10.9021203
3.68-3.9663.60.91258
3.46-3.6862.70.8941359
3.27-3.4663.30.8851467
3.11-3.27640.8681525
2.97-3.11650.8711586
2.85-2.9763.20.8481695
2.74-2.8565.30.8531727
2.64-2.7466.20.8381835
2.55-2.6467.90.8481843
2.48-2.5569.60.8271969
2.4-2.4867.20.8391988
2.34-2.470.60.8462038
2.28-2.3470.40.8462106
2.22-2.2873.40.8272174
2.17-2.2274.60.8362179
2.12-2.1774.70.8372305
2.07-2.1274.60.8242248
2.03-2.0776.80.8472415
1.99-2.0379.40.842417
1.95-1.9979.70.8292448
1.92-1.9579.90.8452536
1.88-1.9281.70.8412464
1.85-1.8883.20.8012567

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.62 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.154 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.908 / SU B: 6.591 / SU ML: 0.088 / SU R Cruickshank DPI: 0.147 / SU Rfree: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2405 5.1 %RANDOM
Rwork0.149 ---
all0.152 47530 --
obs0.152 47530 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.86 Å2 / Biso mean: 19.83 Å2 / Biso min: 2.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-1.2 Å2
2---0.75 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5172 0 12 451 5635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215391
X-RAY DIFFRACTIONr_bond_other_d0.0010.023607
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9527336
X-RAY DIFFRACTIONr_angle_other_deg0.91538749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37522.88250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56115887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1441552
X-RAY DIFFRACTIONr_chiral_restr0.0870.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
X-RAY DIFFRACTIONr_mcbond_it0.7911.53376
X-RAY DIFFRACTIONr_mcbond_other0.2231.51391
X-RAY DIFFRACTIONr_mcangle_it1.45625406
X-RAY DIFFRACTIONr_scbond_it2.63432015
X-RAY DIFFRACTIONr_scangle_it4.274.51915
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 167 -
Rwork0.18 3338 -
all-3505 -
obs--99.91 %
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)
11.1451-0.5466-0.3281.08370.3941.50560.02530.0269-0.1351-0.1207-0.01320.34940.1763-0.0533-0.01220.1301-0.0264-0.01450.02310.00680.17371.2154.581816.9346
20.6238-0.17770.04691.3435-0.30190.12110.09410.1334-0.0308-0.3665-0.08040.02380.09780.0782-0.01370.13260.05090.01350.0961-0.01020.031814.73353.7906-0.2267
31.14010.36191.3781.97181.77754.4422-0.10350.4011-0.1181-0.16270.2907-0.1711-0.21310.6535-0.18720.0197-0.0420.02510.2186-0.01940.0452-2.685476.2814-12.0977
41.1081-0.38361.04340.7876-0.60061.6168-0.01750.0030.00830.00250.01880.0246-0.0187-0.0672-0.00130.00780.00110.0020.0196-0.00840.0131-6.276976.3625.138
50.8523-0.9043-0.17132.14350.56650.8221-0.0292-0.0671-0.01040.1419-0.0063-0.01390.08580.00040.03550.0175-0.004-0.00550.02720.0060.016310.293662.075421.853
60.5586-0.34880.49762.2433-0.24881.3696-0.0346-0.01020.03840.4348-0.0274-0.3379-0.1142-0.03490.0620.0963-0.0055-0.06780.0294-0.00770.099428.22839.973929.5257
70.3377-0.4720.28652.9999-1.26721.55360.07390.0362-0.0175-0.0984-0.1262-0.1890.06960.08010.05230.01830.01060.00690.02150.01630.075326.106128.885719.3023
84.6401-6.78784.242311.6834-7.50535.1319-0.1398-0.1991-0.04220.34430.27710.1956-0.1282-0.2109-0.13730.0528-0.01090.00620.01750.01190.047518.932823.18926.5505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 30
2X-RAY DIFFRACTION2A31 - 163
3X-RAY DIFFRACTION3A164 - 258
4X-RAY DIFFRACTION4A259 - 348
5X-RAY DIFFRACTION5B18 - 124
6X-RAY DIFFRACTION6B125 - 236
7X-RAY DIFFRACTION7B237 - 330
8X-RAY DIFFRACTION8B331 - 349

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