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- PDB-6kfm: Amino-transferase (AMT) Domain of Hybrid Polyketide/Non-Ribosomal... -

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Basic information

Entry
Database: PDB / ID: 6kfm
TitleAmino-transferase (AMT) Domain 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


transaminase activity / phosphopantetheine binding / ligase activity / 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
Similarity search - Function
Condensation domain / Condensation domain / Amino acid adenylation domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain ...Condensation domain / Condensation domain / Amino acid adenylation domain / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Mycosubtilin synthase subunit A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)103,5886
Polymers102,9092
Non-polymers6784
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-64 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.534, 89.492, 136.880
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
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
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: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 110351 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 20.88 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Χ2: 0.928 / Net I/σ(I): 27.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 3 / Num. unique obs: 5395 / CC1/2: 0.87 / Rpim(I) all: 0.231 / Rrim(I) all: 0.811 / Χ2: 0.808 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.13-2988refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HDM

5hdm


Resolution: 1.7→45.23 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2255 1736 -
Rwork0.1978 --
obs0.1982 107029 96.79 %
Displacement parametersBiso mean: 14.73 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7068 0 42 718 7828
LS refinement shellResolution: 1.7→1.761 Å
RfactorNum. reflection% reflection
Rfree0.303 --
Rwork0.2538 --
obs-8667 79.23 %

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