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- PDB-6uv6: AtmM with bound rebeccamycin analogue -

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Basic information

Entry
Database: PDB / ID: 6uv6
TitleAtmM with bound rebeccamycin analogue
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
Chem-BY9 / S-ADENOSYL-L-HOMOCYSTEINE / D-glucose O-methyltransferase
Similarity search - Component
Biological speciesActinomadura melliaura (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 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 AtmM Bound with Glycosylated Indolocarbazole
Authors: Alvarado, S.K. / Miller, M.D. / Wang, Z. / Thorson, J.S. / Phillips Jr., G.N.
History
DepositionNov 1, 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_author / database_2
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _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
C: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6249
Polymers86,0083
Non-polymers2,6166
Water36020
1
A: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5413
Polymers28,6691
Non-polymers8722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5413
Polymers28,6691
Non-polymers8722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-glucose O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5413
Polymers28,6691
Non-polymers8722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.590, 129.050, 129.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 6 - 268 / Label seq-ID: 6 - 268

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 6 or (resid 7 and (name...AA
2chain 'B'BB
3(chain 'C' and (resid 6 or (resid 7 and (name...CC

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Components

#1: Protein D-glucose O-methyltransferase


Mass: 28669.395 Da / Num. of mol.: 3
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BY9 / 12-beta-D-glucopyranosyl-12,13-dihydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5,7(6H)-dione / rebeccamycin analogue


Mass: 487.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H21N3O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M magnesium chloride hexahydrate, 0.1M HEPES PH7.5, 22%w/v Poly(acrylic acid sodium salt) 5100

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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: 2.72→55.63 Å / Num. obs: 28530 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.071 / Rrim(I) all: 0.181 / Net I/σ(I): 7.8 / Num. measured all: 192029 / Scaling rejects: 67
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
2.72-2.796.71.8581406621010.3420.7762.0161100
12.17-55.635.80.03921883770.9990.0180.04325.898.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.65 Å55.63 Å
Translation3.65 Å55.63 Å

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
XDSMarch 15, 2019data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bus

3bus


Resolution: 2.72→55.63 Å / SU ML: 0.4519 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.2253
RfactorNum. reflection% reflection
Rfree0.2554 1403 4.93 %
Rwork0.2141 --
obs0.2161 28463 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.86 Å2
Refinement stepCycle: LAST / Resolution: 2.72→55.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5931 0 186 20 6137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386240
X-RAY DIFFRACTIONf_angle_d0.79068489
X-RAY DIFFRACTIONf_chiral_restr0.0577946
X-RAY DIFFRACTIONf_plane_restr0.00421291
X-RAY DIFFRACTIONf_dihedral_angle_d14.16373803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.820.39381400.36182684X-RAY DIFFRACTION99.96
2.82-2.930.34291510.33742658X-RAY DIFFRACTION99.82
2.93-3.060.34051570.3082626X-RAY DIFFRACTION99.82
3.06-3.230.31351290.30562673X-RAY DIFFRACTION99.93
3.23-3.430.36481150.29442702X-RAY DIFFRACTION99.68
3.43-3.690.31891420.24842679X-RAY DIFFRACTION99.86
3.69-4.060.24321430.2052685X-RAY DIFFRACTION99.82
4.06-4.650.19951360.17112723X-RAY DIFFRACTION99.9
4.65-5.860.21581570.17552725X-RAY DIFFRACTION99.86
5.86-55.630.22751330.1732905X-RAY DIFFRACTION99.54
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)
11.28505606929-0.199161718558-0.4357800397411.448518121161.378028105311.358350145680.0944948129122-0.1799717913580.5055823339150.381744570280.1932908900550.369200675291-0.6602979504890.2901879600640.0001354611901430.7745371796860.0253077560624-0.0116103669240.778022819842-0.08994344934120.58998445558223.1109351773.2423434396-11.9833207986
21.81887641878-0.701497719062-0.5971155852032.30940699231.11304878312.57310121420.09778246903830.157242895319-0.04846928676480.0175236162737-0.04647794871940.0706063448689-0.202744440172-0.1555785970.0001220942489810.6108883135420.0298123460998-0.04954166999880.571228902552-0.01091008722750.59957033763319.3790807829-1.9654962282-23.8400957551
32.52114007103-0.150385093446-0.5229360039481.02645682066-0.6122415778191.012518606270.141866070855-0.1445483627140.2224293484440.329361161692-0.1787682900390.223190462244-0.29401746229-0.3085601132290.0001715663445690.7108562466320.0184332167465-0.006322396578740.5274591981140.07289064006650.57414336356615.10104965996.22852972498-11.3302802838
41.12943322818-0.258697044635-0.2290947386480.647405640247-0.7911819544911.243305117570.213426877841.100781861540.0933728651575-0.718352994863-0.7286172242550.758692291843-0.166145040002-0.183238017434-0.000126263093350.8481690938860.0273830087414-0.005074748977390.8167672811470.09091063444510.88143275506643.8973545171-15.8334578956-57.3400484697
52.60339918918-0.5259686489730.6006460306421.90335540097-1.015194425063.543972219180.01923899698060.05103923794130.00588903543304-0.254023879354-0.0835493207347-0.1128518357660.03430661354690.199595015922-7.20061746832E-60.6358945642380.004542967118650.02266042143550.529794903225-0.03898691931550.59694363399439.2073588164-22.6373089914-49.4572368573
60.054742184391-0.0176362001193-0.07665411963840.0348687041110.04098444637810.1065677075880.758885108707-0.656241625673-0.7456420659471.10494703712-0.081113770332-0.6887064687160.185855853363-0.80338340943-0.001144608881741.60586051956-0.0321686187847-0.1381077824741.121302402340.07190326799781.223741520392.39533793441-46.5166201377-7.6111824238
71.67299108774-0.059143887602-0.9330617702510.848128036264-0.6111117519271.3561798697-0.2727285512090.0445325667615-0.606316468963-0.0613875260459-0.0526795331032-0.3745820027360.3612047344780.2100491003410.001279076809790.788377350796-0.005172479006840.06803371881460.663519086210.006896927604080.9663020305685.63222827933-36.3387317196-22.8769026647
82.983808070971.04085428676-0.5168490334583.788008613150.2463101980912.206072268170.120091146239-0.483596436176-0.1701890141810.416251805207-0.188478984997-0.06928597372630.396396219318-0.140878795333-0.0007078856888480.772339672879-0.0232330616664-0.009418392841010.79909575454-0.02751161071250.754886942607-2.65242741213-31.694652938-14.4908173144
90.371507760723-0.07626619914920.1969116854790.276193404897-0.005745987386930.103244966476-0.280629967551-0.855496649996-1.128665619430.1701677390920.112384597984-0.2595021565711.23128740125-0.7001387730130.00184591052531.38303564031-0.03903078167550.1070790667071.230656115190.09260772267881.44885480603-2.43638458473-54.7246949814-16.3718622662
100.812021451433-0.309627233988-0.3944765496610.1290198988040.2401469744450.7973253607750.5014205142690.1254732123070.2885862090460.179758293811-0.6777578467180.5188789861470.423734889372-0.415067075555-0.0001983946693880.71606649007-0.0379829696089-0.005387070115660.682868497201-0.03577007170640.652212394129-7.72099522808-32.4424668359-23.7874152749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 228 )
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 268 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 36 )
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 268 )
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 19 )
7X-RAY DIFFRACTION7chain 'C' and (resid 20 through 68 )
8X-RAY DIFFRACTION8chain 'C' and (resid 69 through 211 )
9X-RAY DIFFRACTION9chain 'C' and (resid 212 through 254 )
10X-RAY DIFFRACTION10chain 'C' and (resid 255 through 268 )

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