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- PDB-6b3b: AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and M... -

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Basic information

Entry
Database: PDB / ID: 6b3b
TitleAprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and Malonate
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. ...: / 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
MALONATE ION / : / S-ADENOSYLMETHIONINE / Carrier domain-containing protein
Similarity search - Component
Biological speciesMoorea bouillonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)75,4735
Polymers74,8261
Non-polymers6484
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.705, 88.337, 136.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 451 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M sodium malonate, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.85→46.985 Å / Num. obs: 61427 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 3.44 % / Biso Wilson estimate: 26.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.115 / Χ2: 1.042 / Net I/σ(I): 7.72 / Num. measured all: 211336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.963.2640.7551.2397770.5680.89395.8
1.96-2.093.40.472.1594430.7740.55498.3
2.09-2.263.5060.2863.6287630.9050.33597.8
2.26-2.473.4060.1975.2579660.9480.23196.5
2.47-2.773.4850.1337.6973250.9760.15697
2.77-3.193.5950.08911.6463440.9890.10495.4
3.19-3.93.3840.0617.1953130.9940.0793.7
3.9-5.53.6540.04922.4441680.9950.05792.9
5.5-46.9853.3980.04722.9323280.9960.05588.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6B3A

6b3a


Resolution: 1.85→46.985 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2183 1998 3.28 %
Rwork0.1828 --
obs0.184 61418 91.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.46 Å2 / Biso mean: 37.3935 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 1.85→46.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 41 447 5531
Biso mean--38.94 37.89 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075228
X-RAY DIFFRACTIONf_angle_d0.8337079
X-RAY DIFFRACTIONf_chiral_restr0.052803
X-RAY DIFFRACTIONf_plane_restr0.005903
X-RAY DIFFRACTIONf_dihedral_angle_d14.7833165
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 (%)
1.8454-1.86970.36011340.35723848398285
1.8697-1.89530.33841430.33054228437193
1.8953-1.92240.32861400.30344127426791
1.9224-1.95110.31851370.28774147428490
1.9511-1.98160.32891430.28334237438095
1.9816-2.0140.31841500.26974394454495
2.014-2.04880.30041460.25664272441894
2.0488-2.0860.27541450.23474331447695
2.086-2.12610.26751470.22134274442195
2.1261-2.16950.23271450.22374325447094
2.1695-2.21670.29371440.21184204434894
2.2167-2.26830.24481430.2034333447694
2.2683-2.3250.24481450.2054261440693
2.325-2.38790.25261390.19034178431792
2.3879-2.45810.23331330.18444005413888
2.4581-2.53750.22471450.18874254439993
2.5375-2.62810.20971450.18454238438393
2.6281-2.73340.24031460.17894182432893
2.7334-2.85770.22481400.17884228436892
2.8577-3.00840.22251390.17294153429292
3.0084-3.19680.19671380.17184092423090
3.1968-3.44360.19671340.16544014414888
3.4436-3.790.19961390.15324035417488
3.79-4.33810.17251380.13614057419590
4.3381-5.46420.14071400.13083996413688
5.4642-47.00020.18141350.15423960409587
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)
12.0032-0.61520.15621.90170.12042.916-0.0847-0.4306-0.07830.42990.3064-0.10420.56180.5988-0.12320.41270.1705-0.03320.4206-0.09890.22310.67620.0665-16.6969
21.9832-0.8829-0.69990.93040.50780.67480.002-0.16120.17970.01540.0447-0.0869-0.08710.0749-0.03870.1841-0.0312-0.00120.144-0.03740.185412.9724-4.9219-46.2791
31.17530.05030.76030.58320.46181.38340.0015-0.06260.0280.0103-0.00230.08810.0102-0.0897-0.00550.1627-0.0220.03860.1457-0.01620.2076-9.0184-11.52-53.5989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 237 )A1 - 237
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 448 )A238 - 448
3X-RAY DIFFRACTION3chain 'A' and (resid 449 through 629 )A449 - 629

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