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- PDB-5es5: Crystal structure of the initiation module of LgrA in the "open" ... -

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Basic information

Entry
Database: PDB / ID: 5es5
TitleCrystal structure of the initiation module of LgrA in the "open" and "closed " adenylation states
ComponentsLinear gramicidin synthetase subunit A
KeywordsLIGASE / NRPS / formylation domain / adenylation domain
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
Luciferase; domain 3 / Luciferase; Domain 3 / Non-ribosomal peptide synthase / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Condensation domain / Condensation domain / Amino acid adenylation domain ...Luciferase; domain 3 / Luciferase; Domain 3 / Non-ribosomal peptide synthase / Formyl transferase, N-terminal domain / 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 / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsReimer, J.M. / Aloise, M.N. / Schmeing, T.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
CitationJournal: Nature / Year: 2016
Title: Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase.
Authors: Reimer, J.M. / Aloise, M.N. / Harrison, P.M. / Schmeing, T.M.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 synthetase subunit A
B: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,3184
Polymers176,1262
Non-polymers1922
Water1629
1
A: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1592
Polymers88,0631
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1592
Polymers88,0631
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)278.844, 278.844, 82.831
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Linear gramicidin synthetase subunit A


Mass: 88063.180 Da / Num. of mol.: 2 / Fragment: UNP residues 2-766
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 3.52 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.92 M AmSO4, 0.1 M bis-Tris pH 5.5, 1% PEG 3350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→46.05 Å / Num. obs: 59121 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 83.36 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.062 / Χ2: 1.081 / Net I/av σ(I): 22.659 / Net I/σ(I): 10.4 / Num. measured all: 231403
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.853.829880.510.7850.981100
2.85-2.93.929380.6120.6660.993100
2.9-2.963.929640.7070.511.0181000.917
2.96-3.023.929450.8040.391.0151000.6970.803
3.02-3.083.929700.8480.321.0291000.5730.659
3.08-3.153.929780.8960.261.0551000.4650.535
3.15-3.233.929350.9410.1931.1171000.3450.397
3.23-3.323.929700.9580.1521.1041000.2690.31
3.32-3.423.929590.9680.1261.1471000.2230.258
3.42-3.533.929340.9780.0991.399.90.1740.201
3.53-3.653.929550.9880.071.1191000.1230.142
3.65-3.83.929760.9920.0561.1999.90.0980.114
3.8-3.973.929560.9940.0451.0051000.0780.09
3.97-4.183.929410.9960.0320.9451000.0560.065
4.18-4.443.929730.9950.0331.1621000.0560.065
4.44-4.793.929150.9950.0321.06399.20.0550.064
4.79-5.273.929680.9960.0271.05399.80.0470.054
5.27-6.03429560.9970.0231.1941000.040.046
6.03-7.59429570.9990.0161.0071000.0280.032
7.59-503.929430.9990.0121.11499.60.020.023

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ES6

5es6


Resolution: 2.8→46.05 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 2961 5.01 %
Rwork0.2267 56149 -
obs0.2285 59110 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 425.81 Å2 / Biso mean: 148.4959 Å2 / Biso min: 60.44 Å2
Refinement stepCycle: final / Resolution: 2.8→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10887 0 10 9 10906
Biso mean--169.13 111.99 -
Num. residues----1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311153
X-RAY DIFFRACTIONf_angle_d0.54415150
X-RAY DIFFRACTIONf_chiral_restr0.0441664
X-RAY DIFFRACTIONf_plane_restr0.0031979
X-RAY DIFFRACTIONf_dihedral_angle_d13.6196670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.84460.41111360.37822663279998
2.8446-2.89360.37121380.367326482786100
2.8936-2.94630.37361400.335526892829100
2.9463-3.00290.34331410.328426862827100
3.0029-3.06420.37631410.329526892830100
3.0642-3.13080.38351420.337826482790100
3.1308-3.20360.3911410.322327102851100
3.2036-3.28370.34521370.308926732810100
3.2837-3.37250.3481430.302126762819100
3.3725-3.47170.3021300.299627062836100
3.4717-3.58370.3031400.271926532793100
3.5837-3.71170.29821310.275127062837100
3.7117-3.86030.26751450.257926552800100
3.8603-4.03580.25281500.23726542804100
4.0358-4.24850.24541430.210926902833100
4.2485-4.51450.25221480.214626442792100
4.5145-4.86270.23921410.18952684282599
4.8627-5.35140.20531610.192426322793100
5.3514-6.12420.26091470.205526852832100
6.1242-7.70990.27811400.198326742814100
7.7099-46.05610.17761260.14942684281099

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