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- PDB-6mfx: Crystal structure of a 4-domain construct of a mutant of LgrA in ... -

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Basic information

Entry
Database: PDB / ID: 6mfx
TitleCrystal structure of a 4-domain construct of a mutant of LgrA in the substrate donation 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 domain / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain ...Non-ribosomal peptide synthase / Formyl transferase, N-terminal domain / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9EF / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / VALINE / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReimer, J.M. / Eivaskhani, M. / 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 1.2Oct 11, 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
Revision 1.3Oct 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

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Assembly

Deposited unit
A: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,9614
Polymers137,9551
Non-polymers1,0063
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-3 kcal/mol
Surface area51820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.449, 73.987, 77.076
Angle α, β, γ (deg.)94.310, 114.860, 92.230
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Linear gramicidin synthase subunit A


Mass: 137955.156 Da / Num. of mol.: 1 / Fragment: UNP residues 2-1198
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-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H26N3O8P
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: 26% PEG4000, 0.1 M Tris-HCl, pH 8.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2017
RadiationMonochromator: 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: 2.2→69.58 Å / Num. obs: 66903 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.64 Å2 / CC1/2: 0.991 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4469 / CC1/2: 0.388 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIXdev_3584refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MFW

6mfw


Resolution: 2.2→69.58 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1973 2.95 %
Rwork0.1949 64869 -
obs0.1963 66842 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.95 Å2 / Biso mean: 54.086 Å2 / Biso min: 13.09 Å2
Refinement stepCycle: final / Resolution: 2.2→69.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9483 0 105 371 9959
Biso mean--51.13 42.55 -
Num. residues----1186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.34991540.2753458496
2.255-2.3160.33381400.2718457097
2.316-2.38420.27181380.2475459997
2.3842-2.46110.30221390.2488459698
2.4611-2.54910.30241310.2393461798
2.5491-2.65110.28961410.2299463998
2.6511-2.77180.2871430.2296461898
2.7718-2.91790.2841420.2285465398
2.9179-3.10080.26961370.2229463598
3.1008-3.34020.29511440.2096467098
3.3402-3.67630.24761390.193465998
3.6763-4.20820.22411370.1635466699
4.2082-5.30160.1551430.1401468399
5.3016-69.580.2071450.1675468099

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