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- PDB-5wmm: Crystal structure of an adenylation domain interrupted by a methy... -

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Basic information

Entry
Database: PDB / ID: 5wmm
TitleCrystal structure of an adenylation domain interrupted by a methylation domain (AMA4) from nonribosomal peptide synthetase TioS
Components
  • MbtH homologue
  • NRPS
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide / Thiocoraline / Depsipeptide / Thiolation / Nucleotidyl transferase / N-methylation
Function / homology
Function and homology information


toxin biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity / metal ion binding / cytosol
Similarity search - Function
Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Methyltransferase domain / Polyketide synthase, thioesterase domain / Thioesterase ...Rubredoxin-like / Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id / MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Methyltransferase domain / Polyketide synthase, thioesterase domain / Thioesterase / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-B6G / S-ADENOSYL-L-HOMOCYSTEINE / MbtH homologue / NRPS
Similarity search - Component
Biological speciesMicromonospora sp. ML1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPang, A.H. / Mori, S. / Garneau-Tsodikova, S. / Tsodikov, O.V.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Structural basis for backbone N-methylation by an interrupted adenylation domain.
Authors: Mori, S. / Pang, A.H. / Lundy, T.A. / Garzan, A. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionJul 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: NRPS
B: MbtH homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,95210
Polymers111,9082
Non-polymers1,0438
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-77 kcal/mol
Surface area39460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.712, 136.712, 228.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein NRPS


Mass: 102016.586 Da / Num. of mol.: 1 / Fragment: Adenylation domain (UNP residues 1902-2806)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. ML1 (bacteria) / Gene: tioS / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ybdZ::aac(3)IV / References: UniProt: Q333U7
#2: Protein MbtH homologue / MbtH-like protein TioT


Mass: 9891.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. ML1 (bacteria) / Gene: tioT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ybdZ::aac(3)IV / References: UniProt: Q333U6

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Non-polymers , 5 types, 12 molecules

#3: Chemical ChemComp-B6G / (2S)-2-amino-3-methylbutanoyl (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl hydrogen (S)-phosphate


Mass: 432.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N6O8P
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.5 Å3/Da / Density % sol: 77.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.12 M calcium chloride, 0.1 M HEPES, pH 7.0, 22% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 20, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 54895 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 18
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.5 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4GR5

4gr5


Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.661 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25316 2855 5.2 %RANDOM
Rwork0.23566 ---
obs0.23657 52034 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.178 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å21.38 Å20 Å2
2--2.75 Å20 Å2
3----8.93 Å2
Refinement stepCycle: 1 / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7277 0 61 4 7342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197517
X-RAY DIFFRACTIONr_bond_other_d0.0060.027108
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.96910268
X-RAY DIFFRACTIONr_angle_other_deg0.908316287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25322.415352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.102151145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7491586
X-RAY DIFFRACTIONr_chiral_restr0.0630.21134
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021739
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0018.4973736
X-RAY DIFFRACTIONr_mcbond_other3.0018.4963735
X-RAY DIFFRACTIONr_mcangle_it5.00112.7394663
X-RAY DIFFRACTIONr_mcangle_other512.7394664
X-RAY DIFFRACTIONr_scbond_it1.5268.6413781
X-RAY DIFFRACTIONr_scbond_other1.5268.643781
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.79812.8765606
X-RAY DIFFRACTIONr_long_range_B_refined6.04866.0737887
X-RAY DIFFRACTIONr_long_range_B_other6.04866.0767888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 207 -
Rwork0.358 3734 -
obs--98.55 %

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