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- PDB-8fx7: Non-ribosomal PCP-C didomain (ester stabilised leucine) acceptor ... -

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Basic information

Entry
Database: PDB / ID: 8fx7
TitleNon-ribosomal PCP-C didomain (ester 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 / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / 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 / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-YCT / Non-ribosomal peptide synthase:Amino acid adenylation
Similarity search - Component
Biological speciesThermobifida fusca YX (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)114,2894
Polymers113,3782
Non-polymers9112
Water6,233346
1
A: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1442
Polymers56,6891
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1442
Polymers56,6891
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.333, 104.782, 106.557
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 PCP-C didomain / Non-ribosomal peptide synthase:Amino acid adenylation


Mass: 56689.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca YX (bacteria) / Strain: YX / Gene: Tfu_1867 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47NR9
#2: Chemical ChemComp-YCT / 2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl L-leucinate


Mass: 455.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H34N3O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
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: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.2→47.492 Å / Num. obs: 59893 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 37.99 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.79
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2 % / Num. unique obs: 5913 / CC1/2: 0.633 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.49 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 2781 4.65 %
Rwork0.1864 --
obs0.1884 59849 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7927 0 58 346 8331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038214
X-RAY DIFFRACTIONf_angle_d0.54111250
X-RAY DIFFRACTIONf_dihedral_angle_d7.8091163
X-RAY DIFFRACTIONf_chiral_restr0.0381302
X-RAY DIFFRACTIONf_plane_restr0.0051501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.28951280.2382800X-RAY DIFFRACTION99
2.24-2.280.26441540.21282811X-RAY DIFFRACTION100
2.28-2.320.28591300.21162787X-RAY DIFFRACTION100
2.32-2.370.26911280.20582840X-RAY DIFFRACTION100
2.37-2.420.25431440.20712837X-RAY DIFFRACTION100
2.42-2.480.28031170.21252815X-RAY DIFFRACTION100
2.48-2.540.27321460.21362833X-RAY DIFFRACTION100
2.54-2.610.28341630.21612806X-RAY DIFFRACTION100
2.61-2.690.30221670.21332801X-RAY DIFFRACTION100
2.69-2.770.26731310.20932822X-RAY DIFFRACTION100
2.77-2.870.27681960.20412780X-RAY DIFFRACTION100
2.87-2.990.24891510.19452864X-RAY DIFFRACTION100
2.99-3.120.24071420.19632821X-RAY DIFFRACTION100
3.12-3.290.24081520.19512833X-RAY DIFFRACTION100
3.29-3.490.23910.17722921X-RAY DIFFRACTION100
3.49-3.760.19751410.17282856X-RAY DIFFRACTION100
3.76-4.140.22031210.16912909X-RAY DIFFRACTION100
4.14-4.740.19861330.1562892X-RAY DIFFRACTION100
4.74-5.970.2146940.17962992X-RAY DIFFRACTION100
5.97-47.490.17951520.18143048X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -30.9404 Å / Origin y: -39.1268 Å / Origin z: 4.9541 Å
111213212223313233
T0.2516 Å2-0.0119 Å20.0273 Å2-0.2712 Å2-0.0198 Å2--0.2361 Å2
L0.072 °2-0.1939 °20.0866 °2-0.8315 °2-0.1769 °2--0.0029 °2
S0.0041 Å °0.0055 Å °0.0386 Å °-0.0687 Å °-0.0139 Å °-0.0805 Å °0.0103 Å °0.0013 Å °0.0083 Å °
Refinement TLS groupSelection details: all

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