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- PDB-6uvq: Crystal structure of Apo AtmM -

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Basic information

Entry
Database: PDB / ID: 6uvq
TitleCrystal structure of Apo AtmM
ComponentsD-glucose O-methyltransferase
KeywordsTRANSFERASE / methyltransferase / natural products / indolocarbazole / SAM
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / Polyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 11 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / D-glucose O-methyltransferase
Similarity search - Component
Biological speciesActinomadura melliaura (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsAlvarado, S.K. / Wang, Z. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM098248 United States
National Science Foundation (NSF, United States)STC 1231306 United States
CitationJournal: To Be Published
Title: Structure of Apo AtmM
Authors: Alvarado, S.K. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionNov 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.title ..._audit_author.name / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,5056
Polymers57,3392
Non-polymers1674
Water8,161453
1
A: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7533
Polymers28,6691
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7533
Polymers28,6691
Non-polymers832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: D-glucose O-methyltransferase
B: D-glucose O-methyltransferase
hetero molecules

A: D-glucose O-methyltransferase
B: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,01112
Polymers114,6784
Non-polymers3338
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10390 Å2
ΔGint-83 kcal/mol
Surface area35640 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-36 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.463, 52.997, 70.842
Angle α, β, γ (deg.)90.000, 93.340, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and ((resid 12 and (name CA or name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA12 - 26812 - 268
21(chain B and ((resid 12 and (name CA or name...BB1212
22(chain B and ((resid 12 and (name CA or name...BB12 - 26812 - 268
23(chain B and ((resid 12 and (name CA or name...BB12 - 26812 - 268

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Components

#1: Protein D-glucose O-methyltransferase


Mass: 28669.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura melliaura (bacteria) / Gene: atM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0H2W9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20M Magnesium acetate, PEG3350 and 2Deoxyadenosine 5triphosphate disodium salt , Benzidine, Carnitine hydrochloride, Sulfanilamide, Cytosine and 0.02M HEPES sodium pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 15, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.84→51.03 Å / Num. obs: 43534 / % possible obs: 97 % / Redundancy: 3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.057 / Rrim(I) all: 0.103 / Net I/σ(I): 6.6 / Num. measured all: 132128 / Scaling rejects: 177
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.892.10.757529625380.4980.6090.977176.9
8.23-51.0330.04316705520.9970.030.05312.899.2

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
DIALS1.8.2-g5331de77-releasedata reduction
Aimless0.7.4data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bus

3bus


Resolution: 1.84→42.411 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 2077 4.78 %
Rwork0.1807 41361 -
obs0.1827 43438 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.99 Å2 / Biso mean: 40.1073 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 1.84→42.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 16 453 4310
Biso mean--27.11 43.92 -
Num. residues----514
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2367X-RAY DIFFRACTION6.563TORSIONAL
12B2367X-RAY DIFFRACTION6.563TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.84-1.88230.35781040.2964211974
1.8823-1.92940.33531010.2899244886
1.9294-1.98160.31481340.2558265795
1.9816-2.03990.29961530.2212279699
2.0399-2.10570.25171600.21792805100
2.1057-2.1810.23581340.19842825100
2.181-2.26830.25831360.19872846100
2.2683-2.37150.22491490.18412823100
2.3715-2.49650.23661430.18562849100
2.4965-2.65290.23331770.17262790100
2.6529-2.85770.19821550.1789281899
2.8577-3.14520.19671400.17842846100
3.1452-3.60010.20151230.1632876100
3.6001-4.5350.18381540.14892872100
4.535-42.4110.24751140.176299199
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)
11.4163-1.2484-0.1311.18180.52652.0139-0.12720.1002-0.23310.0842-0.03040.5370.125-0.4459-0.00720.2606-0.0168-0.02180.3819-0.08230.42389.4538-23.392723.1024
21.5873-0.4658-0.30961.17580.62832.10750.0136-0.0351-0.17090.0042-0.043-0.00440.24090.028100.23720.00050.01210.1889-0.02260.272124.7909-26.023129.9863
31.5866-0.73020.54721.7632-0.41471.81720.05650.272-0.0114-0.3065-0.17270.04720.0617-0.069-0.00130.27020.02920.00430.2642-0.04460.215221.4717-19.924612.2995
40.41230.2736-0.43810.4713-0.18460.61150.0534-0.10930.15080.4575-0.05220.45330.2285-0.3728-0.00170.33270.0685-0.0830.4219-0.06180.43714.7192-13.874426.5242
50.3670.01150.51330.41830.95852.8379-0.26970.43580.4854-0.2830.20650.024-1.14120.39440.01690.37620.0481-0.06180.4701-0.03360.37527.0228-6.262622.7102
60.44480.16180.1350.2925-0.29361.19730.30430.3632-0.4957-0.5475-0.17930.16940.2665-0.02050.00350.27660.0145-0.03360.3389-0.09010.261116.1066-25.068511.0254
70.93030.8463-0.12860.7643-0.09290.46260.0539-0.10610.1571-0.008-0.15910.02520.018-0.3130.00020.2819-0.02740.03350.358-0.09660.291313.316-8.990447.9373
80.5117-0.33960.76451.56340.13932.21540.0245-0.16830.28750.1014-0.07180.2604-0.2632-0.3771-0.00650.29330.03610.02230.2761-0.07890.39814.85844.981246.7098
90.27960.2541-0.15640.2559-0.15270.5067-0.12380.00890.1577-0.04920.17270.0207-0.2356-0.156400.271-0.0042-0.00560.1985-0.03650.291222.85332.954842.0645
100.7134-0.1288-0.0410.29560.54581.0597-0.04770.05820.1485-0.012-0.0576-0.2416-0.25780.243600.2316-0.01-0.03310.1998-0.01720.271325.7679-3.081635.9427
110.77770.5675-0.22450.9035-0.25491.63570.0845-0.23640.02360.2041-0.2326-0.0214-0.10660.0965-00.2853-0.0384-0.00820.243-0.05330.260727.5057-1.985654.7822
120.35660.0410.04820.1129-0.1520.2728-0.039-0.529-0.18430.31780.08670.35750.4129-0.13050.01580.4138-0.10270.12140.5097-0.06370.36077.441-17.598961.9415
130.54140.16540.03520.1672-0.21350.59320.0898-0.36530.21350.5482-0.19910.0732-0.072-0.00470.00010.4185-0.08290.00810.3889-0.09790.288919.6992-1.467463.2332
140.3655-0.19110.24580.3608-0.35540.357-0.08410.0233-0.2346-0.0311-0.07160.2820.13-0.2983-0.00010.359-0.05130.06310.4488-0.07660.47244.8149-11.061244.3156
150.30930.0217-0.05520.1988-0.02640.341-0.3869-0.3787-0.45650.02810.19250.07640.95470.1191-0.00010.4556-0.07530.0860.4466-0.04610.40317.0722-18.757248.0389
160.3912-0.2120.37830.2271-0.48390.9710.0439-0.34020.21410.4122-0.04390.0877-0.1726-0.072-0.00030.337-0.0460.0710.3463-0.13710.334616.12740.222459.6487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 51 )A12 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 112 )A52 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 211 )A113 - 211
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 237 )A212 - 237
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 254 )A238 - 254
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 268 )A255 - 268
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 29 )B12 - 29
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 68 )B30 - 68
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 88 )B69 - 88
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 112 )B89 - 112
11X-RAY DIFFRACTION11chain 'B' and (resid 113 through 164 )B113 - 164
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 183 )B165 - 183
13X-RAY DIFFRACTION13chain 'B' and (resid 184 through 211 )B184 - 211
14X-RAY DIFFRACTION14chain 'B' and (resid 212 through 237 )B212 - 237
15X-RAY DIFFRACTION15chain 'B' and (resid 238 through 254 )B238 - 254
16X-RAY DIFFRACTION16chain 'B' and (resid 255 through 268 )B255 - 268

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