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- PDB-6mfw: Crystal structure of a 4-domain construct of LgrA in the substrat... -

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Basic information

Entry
Database: PDB / ID: 6mfw
TitleCrystal structure of a 4-domain construct of LgrA in the substrate donation state
ComponentsLinear gramicidin synthase subunit A
KeywordsLIGASE / nonribosomal peptide synthetase / tailoring domain / NRPS / enzyme / natural product / linear gramicidin
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / ligase activity / 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 / 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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / 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 / Chem-JQG / PHOSPHATE ION / VALINE / Linear gramicidin synthase subunit A
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReimer, J.M. / Eivaskhani, M. / Schmeing, T.M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)106615 Canada
Other government Canada
CitationJournal: Science / Year: 2019
Title: Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility.
Authors: Reimer, J.M. / Eivaskhani, M. / Harb, I. / Guarne, A. / Weigt, M. / Schmeing, T.M.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Linear gramicidin synthase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,7407
Polymers138,0571
Non-polymers1,6836
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-14 kcal/mol
Surface area50750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.370, 133.870, 162.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Linear gramicidin synthase subunit A


Mass: 138057.391 Da / Num. of mol.: 1 / Fragment: UNP residues 2-1198
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

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Non-polymers , 7 types, 185 molecules

#2: Chemical ChemComp-JQG / (2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-butanamide


Mass: 467.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H32N4O9P
#3: 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
#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: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: Protein + 2.5 mM AMPcPP + 2.5 mM valine + 2 mM N5-fTHF in 2.5 mM magnesium chloride, 15% PEG4000, 100 mM Tris, pH 7.78, 25 mM Tris, pH 7.5, 100 mM sodium chloride equilibrated against a ...Details: Protein + 2.5 mM AMPcPP + 2.5 mM valine + 2 mM N5-fTHF in 2.5 mM magnesium chloride, 15% PEG4000, 100 mM Tris, pH 7.78, 25 mM Tris, pH 7.5, 100 mM sodium chloride equilibrated against a reservoir containing 2.5 mM magnesium chloride, 18% PEG4000, 150 mM sodium chloride, 100 mM Tris, pH 7.7, drops streak-seeded from a seed stock of LgrA (F-A-PCP-C) crystals

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→69.333 Å / Num. obs: 50890 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 40.8 Å2 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.58 Å / Num. unique obs: 4629 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5ES5

5es5


Resolution: 2.5→69.333 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31
RfactorNum. reflection% reflection
Rfree0.2435 2000 3.94 %
Rwork0.2004 --
obs0.2021 50802 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→69.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9411 0 109 179 9699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049729
X-RAY DIFFRACTIONf_angle_d0.67213214
X-RAY DIFFRACTIONf_dihedral_angle_d18.7583587
X-RAY DIFFRACTIONf_chiral_restr0.0471476
X-RAY DIFFRACTIONf_plane_restr0.0031707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.34681410.30773461X-RAY DIFFRACTION100
2.5625-2.63180.33931400.28793407X-RAY DIFFRACTION100
2.6318-2.70930.34941400.28063424X-RAY DIFFRACTION100
2.7093-2.79670.32361420.26913447X-RAY DIFFRACTION100
2.7967-2.89670.30021420.25863466X-RAY DIFFRACTION100
2.8967-3.01260.31911410.24893434X-RAY DIFFRACTION100
3.0126-3.14980.28021410.23453454X-RAY DIFFRACTION100
3.1498-3.31580.28091430.22353467X-RAY DIFFRACTION100
3.3158-3.52360.24371410.20573465X-RAY DIFFRACTION100
3.5236-3.79560.24991420.20363463X-RAY DIFFRACTION100
3.7956-4.17750.20711450.16923522X-RAY DIFFRACTION100
4.1775-4.78190.20291440.14613527X-RAY DIFFRACTION100
4.7819-6.02410.2091450.17123558X-RAY DIFFRACTION100
6.0241-69.35920.20031530.18043707X-RAY DIFFRACTION100

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