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- PDB-5n81: Crystal structure of an engineered TycA variant in complex with a... -

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Basic information

Entry
Database: PDB / ID: 5n81
TitleCrystal structure of an engineered TycA variant in complex with an O-propargyl-beta-Tyr-AMP analog
ComponentsTyrocidine synthase 1
KeywordsLIGASE / nonribosomal peptide synthetase / adenylation domain
Function / homology
Function and homology information


phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / ligase activity / antibiotic biosynthetic process / ATP binding
Similarity search - Function
AMP-binding / Non-ribosomal peptide synthase / ANL, N-terminal domain / 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 ...AMP-binding / Non-ribosomal peptide synthase / ANL, N-terminal domain / 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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8Q2 / Tyrocidine synthase 1
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNiquille, D.L. / Hansen, D.A. / Mori, T. / Fercher, D. / Kries, H. / Hilvert, D.
CitationJournal: Nat Chem / Year: 2018
Title: Nonribosomal biosynthesis of backbone-modified peptides.
Authors: Niquille, D.L. / Hansen, D.A. / Mori, T. / Fercher, D. / Kries, H. / Hilvert, D.
History
DepositionFeb 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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: Tyrocidine synthase 1
B: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8707
Polymers95,3742
Non-polymers1,4965
Water15,277848
1
A: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3313
Polymers47,6871
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5404
Polymers47,6871
Non-polymers8533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.574, 60.245, 247.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrocidine synthase 1 / Tyrocidine synthase I


Mass: 47687.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: tycA / Production host: Escherichia coli (E. coli)
References: UniProt: P09095, phenylalanine racemase (ATP-hydrolysing)
#2: Chemical ChemComp-8Q2 / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate


Mass: 547.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N7O8S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 848 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris (pH 5.5) containing 200 mM (NH4)2SO4, 25% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→49.56 Å / Num. obs: 118720 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5829 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1amu

1amu


Resolution: 1.6→43.19 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.08
RfactorNum. reflection% reflection
Rfree0.2006 2011 1.7 %
Rwork0.1757 --
obs0.1761 118611 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 100 848 7153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066434
X-RAY DIFFRACTIONf_angle_d0.8838743
X-RAY DIFFRACTIONf_dihedral_angle_d15.783909
X-RAY DIFFRACTIONf_chiral_restr0.0661001
X-RAY DIFFRACTIONf_plane_restr0.0051111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28061410.24638197X-RAY DIFFRACTION100
1.64-1.68440.30131450.22978223X-RAY DIFFRACTION100
1.6844-1.73390.25571390.20878257X-RAY DIFFRACTION100
1.7339-1.78990.22511450.19838221X-RAY DIFFRACTION100
1.7899-1.85390.22011430.19298244X-RAY DIFFRACTION100
1.8539-1.92810.2351380.18248293X-RAY DIFFRACTION100
1.9281-2.01580.23381430.17878261X-RAY DIFFRACTION100
2.0158-2.12210.2211390.17458298X-RAY DIFFRACTION100
2.1221-2.25510.19311480.17048252X-RAY DIFFRACTION100
2.2551-2.42920.20371410.17668334X-RAY DIFFRACTION100
2.4292-2.67360.1931390.18468353X-RAY DIFFRACTION100
2.6736-3.06040.22371470.17858407X-RAY DIFFRACTION100
3.0604-3.85540.1841490.1618479X-RAY DIFFRACTION100
3.8554-43.20590.1571540.15868781X-RAY DIFFRACTION100

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