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- PDB-7ywj: Crystal structure of an engineered TycA variant, TycA pPLA (L313P) -

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Basic information

Entry
Database: PDB / ID: 7ywj
TitleCrystal structure of an engineered TycA variant, TycA pPLA (L313P)
ComponentsTyrocidine synthase 1
KeywordsLIGASE / Nonribosomal peptide synthetase / Adenylation domain / depsipeptides
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 / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / 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 / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / 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
Tyrocidine synthase 1
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 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)95,7407
Polymers95,0932
Non-polymers6465
Water19,2581069
1
A: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8874
Polymers47,5471
Non-polymers3413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrocidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8523
Polymers47,5471
Non-polymers3052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.043, 60.419, 249.243
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrocidine synthase 1 / Tyrocidine synthase I


Mass: 47546.734 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.26 %
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, and di-sodium malonate (1 M)

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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: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.749→48.9 Å / Num. obs: 92757 / % possible obs: 99.98 % / Redundancy: 13.2 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1196 / Rpim(I) all: 0.034 / Rrim(I) all: 0.1244 / Net I/σ(I): 16.51
Reflection shellResolution: 1.749→1.812 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 9168 / CC1/2: 0.378 / % possible all: 99.92

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMU

1amu


Resolution: 1.749→48.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 4638 5 %RANDOM
Rwork0.175 ---
obs0.1767 92752 100 %-
Displacement parametersBiso max: 84.12 Å2 / Biso mean: 34.24 Å2 / Biso min: 18 Å2
Baniso -1Baniso -2Baniso -3
1-2.9719 Å20 Å20 Å2
2---0.0169 Å20 Å2
3----2.955 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.749→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 39 1069 7324
Biso mean--42.27 45.31 -
Num. residues----796
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2287SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1116HARMONIC5
X-RAY DIFFRACTIONt_it6549HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6988SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6549HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8916HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion15.18
LS refinement shellResolution: 1.75→1.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2658 93 5.01 %
Rwork0.2447 1763 -
all0.2458 1856 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83510.30840.44110.65130.21610.66580.00020.02730.01140.0451-0.0006-0.0152-0.01180.060.0004-0.22360.0058-0.0129-0.17530.0034-0.196210.4678-5.7655-47.6491
20.43120.2318-0.0910.7158-0.22170.4578-0.01490.05190.0258-0.01620.0099-0.0103-0.03270.03420.005-0.1106-0.0044-0.0152-0.15460.0019-0.166537.6272-33.6655-13.5921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 428
2X-RAY DIFFRACTION2{ B|* }B29 - 428

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