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

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Basic information

Entry
Database: PDB / ID: 6uwd
TitleCrystal structure of Apo AtmM
ComponentsD-glucose O-methyltransferase
KeywordsTRANSFERASE / methyltransferase / natural products / indolocarbazole / SAM
Function / homologyPolyketide synthase, methyltransferase domain / Methyltransferase in polyketide synthase (PKS) enzymes. / Methyltransferase type 11 / Methyltransferase domain / S-adenosylmethionine-dependent methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ACETATE ION / D-glucose O-methyltransferase
Function and homology information
Biological speciesActinomadura melliaura (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 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. / Wang, Z. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionNov 5, 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7533
Polymers28,6691
Non-polymers832
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, gel filtration supports monomeric assignment in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: D-glucose O-methyltransferase
hetero molecules

A: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5056
Polymers57,3392
Non-polymers1674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2950 Å2
ΔGint-34 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.620, 118.620, 62.443
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein D-glucose O-methyltransferase


Mass: 28669.395 Da / Num. of mol.: 1
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 / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.42 Å3/Da / Density % sol: 72.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20M Magnesium acetate, 16% PEG 3350 and 10% of ATP disodium salt, Benzidine, L-Carnitine hydrochloride, Sulfanilamide, Cytosine in 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: 1.03326 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 26, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 2.04→102.73 Å / Num. obs: 32348 / % possible obs: 99.6 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.019 / Rrim(I) all: 0.06 / Net I/σ(I): 17.8 / Num. measured all: 317358 / Scaling rejects: 256
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
2.04-2.099.11.3922110223280.6880.4871.4771.597.4
9.12-102.738.80.03136374130.9990.0110.03355.2100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.04 Å102.73 Å
Translation2.04 Å102.73 Å

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
DIALS1.12.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bus

3bus


Resolution: 2.04→59.31 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1921 6.25 %
Rwork0.1878 28832 -
obs0.189 30753 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.89 Å2 / Biso mean: 68.3605 Å2 / Biso min: 39.12 Å2
Refinement stepCycle: final / Resolution: 2.04→59.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 8 83 2013
Biso mean--52.5 64.75 -
Num. residues----257
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.04-2.0910.26111150.2979173279
2.091-2.14750.29941140.271183785
2.1475-2.21070.28861280.2529186887
2.2107-2.28210.24081340.2354197192
2.2821-2.36360.22761350.2143200693
2.3636-2.45830.241360.2178204195
2.4583-2.57020.24311380.2144213198
2.5702-2.70570.24951390.205210798
2.7057-2.87520.20711460.2112212498
2.8752-3.09720.23131480.2089215599
3.0972-3.40880.21691430.2027217199
3.4088-3.9020.20771480.18412193100
3.902-4.91570.17331420.15032213100
4.9157-59.310.19481550.1732283100
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)
12.6826-0.3517-0.38420.9982-0.05812.74360.0279-0.1879-0.2240.0765-0.08630.26170.1727-0.2541-0.00010.49510.01920.01240.5161-0.00110.569440.280936.19626.1
20.4322-0.0521-0.2260.43760.31440.7095-0.0308-0.58020.240.2167-0.0649-0.071-0.0876-0.187600.481-0.00390.02120.55860.0240.469844.270143.521631.8404
33.1364-0.538-0.68781.71520.46441.85350.1340.2860.0821-0.2772-0.14280.1062-0.2816-0.17460.00190.50630.0659-0.01610.47230.04460.438643.039444.031917.7043
41.0611-0.9927-0.64081.9610.27252.1725-0.03950.6278-0.422-0.2324-0.11410.578-0.0761-0.7219-0.00280.54790.0248-0.06230.7007-0.08270.746529.237235.348519.2417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 68 )A12 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 88 )A69 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 211 )A89 - 211
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 268 )A212 - 268

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