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- PDB-6ulz: Adenylation domain of the initiation module of LgrA mutant P483M -

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Basic information

Entry
Database: PDB / ID: 6ulz
TitleAdenylation domain of the initiation module of LgrA mutant P483M
ComponentsLinear gramicidin synthase subunit A
KeywordsBIOSYNTHETIC PROTEIN / NRPS / Nonribosomal peptide synthetase / non-ribosomal peptide synthetase / adenylation / adenylation domain / natural product / adenylate
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / cytosol
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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / FORMIC ACID / 3-METHYL-2-OXOBUTANOIC ACID / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsChiche-Lapierre, C. / Alonzo, D.A. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis.
Authors: Alonzo, D.A. / Chiche-Lapierre, C. / Tarry, M.J. / Wang, J. / Schmeing, T.M.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 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

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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)78,5056
Polymers77,7451
Non-polymers7595
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint3 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.180, 161.180, 138.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Linear gramicidin synthase subunit A


Mass: 77745.492 Da / Num. of mol.: 1 / Fragment: initiation module (UNP residues 2-684) / Mutation: P483M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: lgrA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70LM7
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-KIV / 3-METHYL-2-OXOBUTANOIC ACID / ALPHA-KETOISOVALERIC ACID / KETOVALINE


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 5.93 Å3/Da / Density % sol: 79.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2.37 M sodium formate, 0.112 M sodium acetate / PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.1→138.6 Å / Num. obs: 33772 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 58.92 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.019 / Net I/σ(I): 24.3
Reflection shellResolution: 3.1→3.25 Å / Redundancy: 26.5 % / Mean I/σ(I) obs: 7.6 / Num. unique obs: 4403 / CC1/2: 0.99 / Rpim(I) all: 0.087 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
DIALSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5ES6

5es6


Resolution: 3.1→113.97 Å / SU ML: 0.3692 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2464 1687 5.01 %
Rwork0.2115 32008 -
obs0.2133 33695 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.67 Å2
Refinement stepCycle: LAST / Resolution: 3.1→113.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4655 0 48 20 4723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00254806
X-RAY DIFFRACTIONf_angle_d0.50726521
X-RAY DIFFRACTIONf_chiral_restr0.0432718
X-RAY DIFFRACTIONf_plane_restr0.0025846
X-RAY DIFFRACTIONf_dihedral_angle_d6.60432872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.190.37811400.31842597X-RAY DIFFRACTION99.93
3.19-3.290.29331360.28382652X-RAY DIFFRACTION99.96
3.29-3.410.30661400.26032605X-RAY DIFFRACTION100
3.41-3.550.29431390.26172629X-RAY DIFFRACTION99.96
3.55-3.710.28241360.23152622X-RAY DIFFRACTION100
3.71-3.910.25471380.20552646X-RAY DIFFRACTION100
3.91-4.150.2231410.1882649X-RAY DIFFRACTION99.93
4.15-4.470.20471410.18072669X-RAY DIFFRACTION100
4.47-4.920.19581400.16732658X-RAY DIFFRACTION100
4.92-5.630.24161400.18332689X-RAY DIFFRACTION99.89
5.63-7.10.24991450.20862724X-RAY DIFFRACTION100
7.1-113.970.21461510.20552868X-RAY DIFFRACTION99.74

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