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- PDB-9be4: The post-condensation state of the dimodular NRPS protein LgrA -

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Basic information

Entry
Database: PDB / ID: 9be4
TitleThe post-condensation state of the dimodular NRPS protein LgrA
ComponentsLinear gramicidin synthase subunit A
KeywordsBIOSYNTHETIC PROTEIN / Nornribosomal peptide synthetase / Condensation / Peptide bond / 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 / Chloramphenicol acetyltransferase-like domain superfamily ...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 / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / 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
: / : / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPistofidis, A. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-178084 Canada
CitationJournal: Nature / Year: 2025
Title: Structures and mechanism of condensation in non-ribosomal peptide synthesis.
Authors: Pistofidis, A. / Ma, P. / Li, Z. / Munro, K. / Houk, K.N. / Schmeing, T.M.
History
DepositionApr 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)413,3507
Polymers412,4932
Non-polymers8575
Water6,305350
1
A: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,9564
Polymers206,2461
Non-polymers7103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,3933
Polymers206,2461
Non-polymers1472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.406, 426.580, 77.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Linear gramicidin synthase subunit A


Mass: 206246.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Complex build by the protein-ligation of the two modules that comprise the first subunit of linear gramicidin synthetase
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli (E. coli) / References: UniProt: Q70LM7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1AMN / N-formyl-L-valyl-N-[2-({N-[(2S)-2-hydroxy-4-{[(S)-hydroxy(oxo)-lambda~5~-phosphanyl]oxy}-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]glycinamide


Mass: 525.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36N5O10P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0M sodium tartrate pH 7.0. 10mM Manganese Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 123053 / % possible obs: 99.8 % / Redundancy: 10.1 % / Biso Wilson estimate: 62.04 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.084 / Rrim(I) all: 0.268 / Χ2: 0.988 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5930 / CC1/2: 0.348 / CC star: 0.719 / Rpim(I) all: 0.551 / Rrim(I) all: 1.558 / Χ2: 0.959 / % possible all: 98.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.21.1_5286refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.87 Å / SU ML: 0.401 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2167
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 2624 2.19 %
Rwork0.218 117460 -
obs0.2189 120084 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.4 Å2
Refinement stepCycle: LAST / Resolution: 3→49.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27708 0 95 350 28153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002828406
X-RAY DIFFRACTIONf_angle_d0.558438607
X-RAY DIFFRACTIONf_chiral_restr0.0434358
X-RAY DIFFRACTIONf_plane_restr0.00515018
X-RAY DIFFRACTIONf_dihedral_angle_d16.608110475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.3802990.35594704X-RAY DIFFRACTION74.95
3.05-3.10.37471320.33935970X-RAY DIFFRACTION94.02
3.1-3.170.33241410.3055958X-RAY DIFFRACTION94.73
3.17-3.240.34251370.29376117X-RAY DIFFRACTION96.16
3.24-3.310.33541380.27826074X-RAY DIFFRACTION96.84
3.31-3.390.3461360.27546231X-RAY DIFFRACTION97.41
3.39-3.490.33541380.2646173X-RAY DIFFRACTION97.56
3.49-3.590.29611410.26046188X-RAY DIFFRACTION98.12
3.59-3.70.33551400.23856312X-RAY DIFFRACTION98.7
3.7-3.840.26851360.22056261X-RAY DIFFRACTION98.42
3.84-3.990.23961410.20856258X-RAY DIFFRACTION98.78
3.99-4.170.24661440.19136324X-RAY DIFFRACTION99.16
4.17-4.390.22171410.18976318X-RAY DIFFRACTION98.82
4.39-4.670.1971400.17426349X-RAY DIFFRACTION99.27
4.67-5.030.22051430.17316377X-RAY DIFFRACTION99.15
5.03-5.530.22091460.19296416X-RAY DIFFRACTION98.81
5.53-6.330.25651400.21386375X-RAY DIFFRACTION98.64
6.33-7.970.24151430.20676483X-RAY DIFFRACTION98.63
7.97-49.870.18911480.18076572X-RAY DIFFRACTION96.03

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