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- PDB-6kfr: Amino-transferase (AMT) Domain - Arg Complex of Hybrid Polyketide... -

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Basic information

Entry
Database: PDB / ID: 6kfr
TitleAmino-transferase (AMT) Domain - Arg Complex of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase
ComponentsMycosubtilin synthase subunit A
KeywordsTRANSFERASE / Amino-transferase / Hybrid Polyketide/Non-Ribosomal Peptide Synthetase
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / transaminase activity / ligase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
CurL-like, PKS C-terminal / Condensation domain / Condensation domain / Amino acid adenylation domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain ...CurL-like, PKS C-terminal / Condensation domain / Condensation domain / Amino acid adenylation domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / AMP-binding enzyme, C-terminal domain superfamily / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Pyridoxal phosphate-dependent transferase, small domain / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / PYRIDOXAL-5'-PHOSPHATE / Mycosubtilin synthase subunit A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTian, Q.W. / Jiang, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570768 China
CitationJournal: To Be Published
Title: Structure Insights into the Molecular Mechanism of Two Tailoring Domains of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase
Authors: Tian, Q.W. / Jiang, T.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.2Mar 12, 2025Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: pdbx_database_related / pdbx_entry_details ...pdbx_database_related / pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycosubtilin synthase subunit A
B: Mycosubtilin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7546
Polymers102,9092
Non-polymers8454
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-64 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.597, 89.650, 134.584
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

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Components

#1: Protein Mycosubtilin synthase subunit A


Mass: 51454.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: mycA / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9R9J1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 312 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 10 mM MgCl2, 5 mM NiCl, 0.1 M HEPES, pH 6.7, 18% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18563 / % possible obs: 96.7 % / Redundancy: 11.7 % / CC1/2: 0.979 / Rpim(I) all: 0.064 / Rrim(I) all: 0.224 / Χ2: 1.024 / Net I/σ(I): 10.43
Reflection shellResolution: 3→3.05 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.83 / Num. unique obs: 776 / CC1/2: 0.781 / Rpim(I) all: 0.279 / Rrim(I) all: 0.907 / Χ2: 0.916 / % possible all: 83.1

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFM

6kfm


Resolution: 3.1→42.53 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2773 1574 -
Rwork0.1756 --
obs0.1858 15746 90.46 %
Displacement parametersBiso mean: 45.29 Å2
Refinement stepCycle: LAST / Resolution: 3.1→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7068 0 52 0 7120
LS refinement shellResolution: 3.1→3.211 Å
RfactorNum. reflection% reflection
Rfree0.3417 --
Rwork0.2186 --
obs-1108 65.45 %

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