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- PDB-5es7: Crystal structure of the F-A domains of the LgrA initiation modul... -

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Basic information

Entry
Database: PDB / ID: 5es7
TitleCrystal structure of the F-A domains of the LgrA initiation module soaked with FON, AMPcPP, and valine.
ComponentsLinear gramicidin synthetase subunit A
KeywordsLIGASE / NRPS / formylation domain / adenylation domain / initiation module
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 / 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 / Chloramphenicol acetyltransferase-like domain superfamily / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Chem-FON / VALINE / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.805 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6794
Polymers77,5831
Non-polymers1,0963
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.943, 160.943, 137.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Linear gramicidin synthetase subunit A


Mass: 77583.281 Da / Num. of mol.: 1 / Fragment: UNP residues 2-684
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-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 5.74 Å3/Da / Density % sol: 78.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2 M Na-formate, 0.1 M Na-Acetate pH 5.3

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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: Nov 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 42877 / % possible obs: 95.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 83.52 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Χ2: 1.127 / Net I/av σ(I): 30 / Net I/σ(I): 10 / Num. measured all: 594075
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.8-2.8511.317280.6720.4931.04878.6
2.85-2.911.717500.7820.3921.05580.1
2.9-2.9611.918600.8580.3061.06184.2
2.96-3.021219480.90.2611.06988.30.9320.969
3.02-3.0812.620150.920.231.07391.90.8270.86
3.08-3.1513.121250.9440.2011.07295.20.7280.756
3.15-3.2313.721330.9670.1571.09797.20.5730.595
3.23-3.321421820.9750.131.14499.10.4780.495
3.32-3.4214.522160.9880.11.18299.90.3710.385
3.42-3.5314.822190.9920.0811.2391000.3010.311
3.53-3.6514.822150.9960.0611.2441000.230.238
3.65-3.814.922110.9970.0471.3211000.1760.183
3.8-3.9714.822350.9980.0341.2961000.1260.13
3.97-4.1814.822280.9990.0251.2051000.0920.095
4.18-4.4414.822370.9990.021.1891000.0760.079
4.44-4.7914.722570.9990.0181.1931000.0660.068
4.79-5.2714.522670.9990.0171.1311000.0630.066
5.27-6.0314.522860.9990.0150.971000.0560.058
6.03-7.5914.423130.9990.0120.9041000.0420.044
7.59-5013.524520.9990.010.93299.90.0340.036

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Processing

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

5es6


Resolution: 2.805→49.982 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2143 5.02 %
Rwork0.2257 40576 -
obs0.2273 42719 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.27 Å2 / Biso mean: 110.9844 Å2 / Biso min: 56.91 Å2
Refinement stepCycle: final / Resolution: 2.805→49.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 0 111 78 4814
Biso mean--117.57 110.61 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044798
X-RAY DIFFRACTIONf_angle_d0.6776514
X-RAY DIFFRACTIONf_chiral_restr0.045714
X-RAY DIFFRACTIONf_plane_restr0.004845
X-RAY DIFFRACTIONf_dihedral_angle_d14.2222840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8054-2.87060.44961130.39882154226777
2.8706-2.94240.46441300.38262281241182
2.9424-3.0220.40561250.38232417254287
3.022-3.11090.39931360.36112571270792
3.1109-3.21130.42631420.33762717285996
3.2113-3.3260.36951510.30352728287999
3.326-3.45910.37521450.291128082953100
3.4591-3.61650.26171470.265827932940100
3.6165-3.80710.26491470.253128232970100
3.8071-4.04560.26411420.213428132955100
4.0456-4.35780.22031480.19032828297699
4.3578-4.7960.20161520.182828272979100
4.796-5.48920.18281510.176528663017100
5.4892-6.91290.23831540.201229123066100
6.9129-49.99010.23731600.198130383198100

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