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- PDB-8fx6: Non-ribosomal PCP-C didomain (amide stabilised leucine) acceptor ... -

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Basic information

Entry
Database: PDB / ID: 8fx6
TitleNon-ribosomal PCP-C didomain (amide stabilised leucine) acceptor bound state
ComponentsPCP-C didomain
KeywordsBIOSYNTHETIC PROTEIN / NRPS / C-domain / PCP-domain
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity / cytosol
Similarity search - Function
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. / Polyketide synthase, phosphopantetheine-binding domain ...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. / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-YCK / Non-ribosomal peptide synthase:Amino acid adenylation
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHo, Y.T.C. / Cryle, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190101272 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1140619 Australia
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Not always an innocent bystander: the impact of stabilised phosphopantetheine moieties when studying nonribosomal peptide biosynthesis.
Authors: Ho, Y.T.C. / Kaczmarski, J.A. / Tailhades, J. / Izore, T. / Steer, D.L. / Schittenhelm, R.B. / Tosin, M. / Jackson, C.J. / Cryle, M.J.
History
DepositionJan 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation_author / diffrn_source
Item: _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PCP-C didomain
B: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4874
Polymers113,5782
Non-polymers9092
Water3,783210
1
A: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2442
Polymers56,7891
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2442
Polymers56,7891
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.719, 105.084, 108.366
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein PCP-C didomain / Non-ribosomal peptide synthase:Amino acid adenylation


Mass: 56789.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1867 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47NR9
#2: Chemical ChemComp-YCK / N-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]-L-leucinamide


Mass: 454.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H35N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 3350, Magnesium formate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95364 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.2→48.16 Å / Num. obs: 61354 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 46.12 Å2 / CC1/2: 0.999 / Net I/σ(I): 8.48
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2 % / Num. unique obs: 6083 / CC1/2: 0.696 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.16 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 3109 5.07 %
Rwork0.2003 58240 -
obs0.2025 61349 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7920 0 58 210 8188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248162
X-RAY DIFFRACTIONf_angle_d0.503511168
X-RAY DIFFRACTIONf_chiral_restr0.03821298
X-RAY DIFFRACTIONf_plane_restr0.00431487
X-RAY DIFFRACTIONf_dihedral_angle_d9.11591155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.42721150.32722651X-RAY DIFFRACTION100
2.23-2.270.35981320.30092620X-RAY DIFFRACTION100
2.27-2.310.33271500.28782585X-RAY DIFFRACTION99.96
2.31-2.350.34931550.27962616X-RAY DIFFRACTION100
2.35-2.40.30211190.26182636X-RAY DIFFRACTION99.96
2.4-2.450.28521730.25392582X-RAY DIFFRACTION100
2.45-2.50.2631950.24532650X-RAY DIFFRACTION100
2.5-2.560.30491510.2532648X-RAY DIFFRACTION100
2.56-2.620.32461310.25482597X-RAY DIFFRACTION99.96
2.62-2.690.28641360.24962649X-RAY DIFFRACTION99.96
2.69-2.770.25741510.24252598X-RAY DIFFRACTION99.96
2.77-2.860.29261430.23992623X-RAY DIFFRACTION100
2.86-2.960.2581540.23092629X-RAY DIFFRACTION100
2.96-3.080.25051480.23182637X-RAY DIFFRACTION100
3.08-3.220.27331590.23662620X-RAY DIFFRACTION100
3.22-3.390.29591200.21942679X-RAY DIFFRACTION100
3.39-3.60.26111300.20862659X-RAY DIFFRACTION100
3.6-3.880.21541560.18192655X-RAY DIFFRACTION100
3.88-4.270.20681440.16682645X-RAY DIFFRACTION100
4.27-4.890.19821570.15592683X-RAY DIFFRACTION100
4.89-6.160.2221400.17632733X-RAY DIFFRACTION100
6.16-48.160.20791500.15232845X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.9180021893 Å / Origin y: 92.1433900709 Å / Origin z: 5.30320783508 Å
111213212223313233
T0.324622279636 Å2-0.0201231640393 Å2-0.055357411194 Å2-0.45573845815 Å20.0641405159009 Å2--0.297760740947 Å2
L0.584269577237 °2-0.302707510237 °2-0.120030559359 °2-0.735841083827 °20.17656158844 °2--0.107565245126 °2
S0.00516595364111 Å °0.0231117099407 Å °-0.182903676922 Å °-0.0807455148142 Å °-0.0286380274891 Å °0.163077902761 Å °0.0389030671483 Å °0.0249552523861 Å °0.0270471087156 Å °
Refinement TLS groupSelection details: all

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