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- PDB-6b39: AprA Methyltransferase 1 - GNAT in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 6b39
TitleAprA Methyltransferase 1 - GNAT in complex with SAH
ComponentsAprA Methyltransferase 1
KeywordsTRANSFERASE / methyltransferase / apratoxin / GCN5 related N-acetyltransferase
Function / homology
Function and homology information


phosphopantetheine binding / transferase activity / metal ion binding
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Carrier domain-containing protein
Similarity search - Component
Biological speciesMoorea bouillonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.392 Å
AuthorsSkiba, M.A. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA108874 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008353 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: A Mononuclear Iron-Dependent Methyltransferase Catalyzes Initial Steps in Assembly of the Apratoxin A Polyketide Starter Unit.
Authors: Skiba, M.A. / Sikkema, A.P. / Moss, N.A. / Tran, C.L. / Sturgis, R.M. / Gerwick, L. / Gerwick, W.H. / Sherman, D.H. / Smith, J.L.
History
DepositionSep 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AprA Methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,26713
Polymers74,8261
Non-polymers1,44112
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-130 kcal/mol
Surface area27630 Å2
Unit cell
Length a, b, c (Å)152.871, 152.871, 95.169
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein AprA Methyltransferase 1


Mass: 74825.836 Da / Num. of mol.: 1 / Mutation: S274I, Q528P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorea bouillonii (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1U7N2Z8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / 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.: 62 / 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: 3.72 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4 M ammonium sulfate, 0.1 M Tris, pH 8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.033
SYNCHROTRONAPS 23-ID-B20.979
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELMar 7, 2017
DECTRIS EIGER X 16M2PIXELMar 7, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
20.9791
ReflectionResolution: 2.39→48.342 Å / Num. obs: 42220 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 7.231 % / Biso Wilson estimate: 64.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.113 / Χ2: 1.24 / Net I/σ(I): 11.78 / Num. measured all: 305308
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.39-2.547.31.7680.849976713968460.3491.90295.9
2.54-2.717.3271.0411.4947067674764240.6291.11895.2
2.71-2.937.220.6052.742800627559280.8510.6594.5
2.93-3.216.9230.315.2637846582154670.9520.33493.9
3.21-3.587.1810.13811.6935469528849390.9910.14993.4
3.58-4.137.5980.08221.533210471343710.9960.08792.7
4.13-5.057.3140.05730.9526980400136890.9980.06192.2
5.05-7.116.9080.05430.6319799317328660.9980.05890.3
7.11-48.3427.1960.03149.6812161191616900.9990.03388.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
RESOLVEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.392→48.342 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 3709 4.75 %
Rwork0.1875 74354 -
obs0.1897 41972 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.57 Å2 / Biso mean: 69.1524 Å2 / Biso min: 38.02 Å2
Refinement stepCycle: final / Resolution: 2.392→48.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 81 62 5178
Biso mean--116.89 58.16 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085224
X-RAY DIFFRACTIONf_angle_d0.9297086
X-RAY DIFFRACTIONf_chiral_restr0.052799
X-RAY DIFFRACTIONf_plane_restr0.005891
X-RAY DIFFRACTIONf_dihedral_angle_d14.6353136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3918-2.42330.41121140.40622405251977
2.4233-2.45640.40481450.36582762290790
2.4564-2.49150.31981480.34132911305992
2.4915-2.52870.3291430.32992890303394
2.5287-2.56820.35671430.31562965310894
2.5682-2.61030.30721460.30442957310395
2.6103-2.65540.37661480.29812924307294
2.6554-2.70360.31161430.28522907305094
2.7036-2.75560.38781440.27532933307794
2.7556-2.81190.30651480.27732927307593
2.8119-2.8730.33151450.27282902304793
2.873-2.93980.3431480.26392900304893
2.9398-3.01330.32721420.27212866300893
3.0133-3.09480.29511450.24892884302992
3.0948-3.18580.30971420.24382850299291
3.1858-3.28870.3021390.22282844298390
3.2887-3.40620.26641420.20922859300192
3.4062-3.54250.23051440.19042912305693
3.5425-3.70370.25711450.18182901304693
3.7037-3.89890.21251420.15442909305193
3.8989-4.1430.19451460.1422874302092
4.143-4.46270.17291500.12512857300792
4.4627-4.91140.16541410.12472862300392
4.9114-5.62120.18821450.1432816296190
5.6212-7.07850.23061330.18342741287488
7.0785-48.35190.17511380.14552796293489
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)
11.6209-0.3083-0.07231.88651.49572.9655-0.0408-0.0855-0.0831-0.04140.03630.3123-0.0981-0.24420.00570.36660.0217-0.07470.39960.1040.569149.228129.598438.5224
23.93522.31970.43444.99070.27420.9199-0.00560.29460.2777-0.41150.05580.1454-0.19290.0938-0.01640.46220.0334-0.02510.42320.05030.388278.097740.662722.1597
32.229-1.1619-0.53052.29160.15571.016-0.0783-0.1352-0.3068-0.04160.0575-0.13980.17350.07560.04470.5124-0.0413-0.03660.42910.01290.535884.336417.802226.7069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -7 through 250 )A-7 - 250
2X-RAY DIFFRACTION2chain 'A' and (resid 251 through 442 )A251 - 442
3X-RAY DIFFRACTION3chain 'A' and (resid 443 through 629 )A443 - 629

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