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- PDB-5es9: Crystal structure of the LgrA initiation module in the formylatio... -

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Basic information

Entry
Database: PDB / ID: 5es9
TitleCrystal structure of the LgrA initiation module in the formylation state
ComponentsLinear gramicidin synthetase subunit A
KeywordsLIGASE / NRPS / formylation domain / adenylation domain / peptidyl carrier protein / initiation module
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 / ANL, C-terminal domain / Condensation domain / Condensation 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 / ANL, C-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ACP-like / 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. / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / GMP Synthetase; Chain A, domain 3 / 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 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)176,4853
Polymers176,1262
Non-polymers3581
Water00
1
A: Linear gramicidin synthetase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4222
Polymers88,0631
Non-polymers3581
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Linear gramicidin synthetase subunit A


Theoretical massNumber of molelcules
Total (without water)88,0631
Polymers88,0631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.057, 162.057, 206.493
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS

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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: 4.51 Å3/Da / Density % sol: 72.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1 M AmSO4, 0.1 M bis-Tris pH 5.5, 3% 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: Jan 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.77→48.45 Å / Num. obs: 32124 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 190.98 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.041 / Net I/av σ(I): 27.219 / Net I/σ(I): 7.3 / Num. measured all: 327215
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.9-3.9711.214460.953100
3.97-4.0411.214520.997100
4.04-4.1211.214430.977100
4.12-4.211.414271.013100
4.2-4.2911.314321.0291000.991
4.29-4.3911.314481.021000.992
4.39-4.511.414471.0141000.723
4.5-4.6211.414621.0271000.582
4.62-4.7611.314361.0761000.421
4.76-4.9111.314531.091000.369
4.91-5.0911.314481.1051000.302
5.09-5.2911.314481.0961000.299
5.29-5.5311.314761.0881000.257
5.53-5.8211.214531.0961000.212
5.82-6.1911.214591.0671000.151
6.19-6.6611.214611.0951000.12
6.66-7.3311.214951.0821000.084
7.33-8.391114781.0691000.062
8.39-10.5510.915141.0181000.045
10.55-501015840.90299.70.038

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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: 3.77→48.45 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.331 1611 5.01 %
Rwork0.3083 30513 -
obs0.3095 32124 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 541.5 Å2 / Biso mean: 261.0343 Å2 / Biso min: 160.85 Å2
Refinement stepCycle: final / Resolution: 3.77→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11504 0 5 0 11509
Biso mean--282.78 --
Num. residues----1440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511775
X-RAY DIFFRACTIONf_angle_d0.91315981
X-RAY DIFFRACTIONf_chiral_restr0.0341759
X-RAY DIFFRACTIONf_plane_restr0.0042085
X-RAY DIFFRACTIONf_dihedral_angle_d13.7094381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.7701-3.8810.57481300.553924942624
3.881-4.00620.52811310.507625062637
4.0062-4.14930.43711280.437125292657
4.1493-4.31530.45691560.425724782634
4.3153-4.51160.40631350.397325232658
4.5116-4.74930.38281210.363625212642
4.7493-5.04650.30421280.327525622690
5.0465-5.43570.36361330.327525092642
5.4357-5.98180.33551290.328125582687
5.9818-6.84530.35691310.326725592690
6.8453-8.61650.32471410.297525912732
8.6165-48.45360.27151480.2426832831

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