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- PDB-6mg0: Crystal structure of a 5-domain construct of LgrA in the thiolati... -

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Basic information

Entry
Database: PDB / ID: 6mg0
TitleCrystal structure of a 5-domain construct of LgrA in the thiolation state
ComponentsLinear gramicidin synthase subunit A
KeywordsLIGASE / nonribosomal peptide synthetase / tailoring domain / NRPS / enzyme / natural product / linear gramicidin
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Non-ribosomal peptide synthase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site ...Non-ribosomal peptide synthase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation 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 / 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
Similarity search - Domain/homology
Chem-DG9 / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsReimer, J.M. / Eivaskhani, M. / Harb, I. / Schmeing, T.M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
Other government Canada
CitationJournal: Science / Year: 2019
Title: Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility.
Authors: Reimer, J.M. / Eivaskhani, M. / Harb, I. / Guarne, A. / Weigt, M. / Schmeing, T.M.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jun 29, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Linear gramicidin synthase subunit A
B: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,7864
Polymers392,2142
Non-polymers1,5722
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.549, 212.894, 253.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 Linear gramicidin synthase subunit A


Mass: 196107.047 Da / Num. of mol.: 2 / Fragment: UNP residues 2-1716
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70LM7
#2: Chemical ChemComp-DG9 / 5'-({[(2R,3R)-3-amino-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-{[oxido(oxo)phosphonio]oxy}butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-4-methylpentyl]sulfonyl}amino)-5'-deoxyadenosine


Mass: 785.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H48N9O12PS2
Has protein modificationY
Nonpolymer detailsDG9 is deprotonated.

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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: 5.78 Å3/Da / Density % sol: 78.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.25 M sodium fluoride, 3.1 M sodium formate, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2017
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 6→78.44 Å / Num. obs: 22451 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 280.3 Å2 / Net I/σ(I): 6.9
Reflection shellResolution: 6→6.48 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4552 / CC1/2: 0.451

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MFW

6mfw


Resolution: 6→78.44 Å / SU ML: 0.95 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.65
RfactorNum. reflection% reflection
Rfree0.2936 1125 5.03 %
Rwork0.2443 --
obs0.2468 22388 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 6→78.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26974 0 100 0 27074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327673
X-RAY DIFFRACTIONf_angle_d0.60137568
X-RAY DIFFRACTIONf_dihedral_angle_d16.46210374
X-RAY DIFFRACTIONf_chiral_restr0.0924183
X-RAY DIFFRACTIONf_plane_restr0.0044879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.0001-6.27310.41051380.35882601X-RAY DIFFRACTION99
6.2731-6.60360.43481390.32862616X-RAY DIFFRACTION100
6.6036-7.01710.36841410.29172622X-RAY DIFFRACTION100
7.0171-7.55850.28431380.2552623X-RAY DIFFRACTION100
7.5585-8.31840.29261350.22892648X-RAY DIFFRACTION100
8.3184-9.52030.25911430.20382681X-RAY DIFFRACTION100
9.5203-11.98770.2361420.20342670X-RAY DIFFRACTION99
11.9877-78.44650.30551490.26172802X-RAY DIFFRACTION99

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