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- PDB-7ywk: Crystal structure of an engineered TycA variant, TycApPLA, in com... -

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Basic information

Entry
Database: PDB / ID: 7ywk
TitleCrystal structure of an engineered TycA variant, TycApPLA, in complex with AMP
ComponentsTyrocidine synthase 1
KeywordsLIGASE / Nonribosomal peptide synthetase / Adenylation domain / depsipeptide
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 / 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-binding / Non-ribosomal peptide synthase / 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
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Tyrocidine synthase 1
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsMittl, P. / Camus, A. / Truong, G. / Markert, G. / Hilvert, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Reprogramming Nonribosomal Peptide Synthetases for Site-Specific Insertion of alpha-Hydroxy Acids.
Authors: Camus, A. / Truong, G. / Mittl, P.R.E. / Markert, G. / Hilvert, D.
History
DepositionFeb 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrocidine synthase 1
B: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,50210
Polymers95,1262
Non-polymers1,3768
Water26,4101466
1
A: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2515
Polymers47,5631
Non-polymers6884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2515
Polymers47,5631
Non-polymers6884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.893, 60.617, 250.537
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tyrocidine synthase 1 / Tyrocidine synthase I


Mass: 47562.777 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)

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Non-polymers , 5 types, 1474 molecules

#2: 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.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1466 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: (NH4)2SO4 (0.2 M), PEG 3,350 (25% (w/v)), BisTris (0.1 M) pH 5.5, NaF (0.5 M) and 10 nL TycApPLA (L313P) seeds

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→43.3 Å / Num. obs: 164330 / % possible obs: 89.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.39 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0348 / Rpim(I) all: 0.0155 / Rrim(I) all: 0.0382 / Net I/σ(I): 25.87
Reflection shellResolution: 1.39→1.44 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 5752 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSJan 31, 2020data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 1.39→43.29 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.394 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1691 8220 5 %RANDOM
Rwork0.1186 ---
obs0.1212 156172 88.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.38 Å2 / Biso mean: 20.005 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2---0.38 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 1.39→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6253 0 86 1466 7805
Biso mean--21.01 36.14 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136813
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176445
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.6399315
X-RAY DIFFRACTIONr_angle_other_deg1.5641.57114905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26323.292319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.678151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0581532
X-RAY DIFFRACTIONr_chiral_restr0.1030.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027854
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021512
X-RAY DIFFRACTIONr_rigid_bond_restr3.42313258
LS refinement shellResolution: 1.39→1.422 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.41 155 -
Rwork0.383 2943 -
obs--22.8 %

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