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- PDB-7kw2: Non-ribosomal didomain (holo-PCP-C) acceptor bound state, R2577G -

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Basic information

Entry
Database: PDB / ID: 7kw2
TitleNon-ribosomal didomain (holo-PCP-C) acceptor bound state, R2577G
ComponentsPCP-C didomain
KeywordsBIOSYNTHETIC PROTEIN / NRPS / C-domain / PCP-domain
Function / homology
Function and homology information


lipid biosynthetic process / phosphopantetheine binding / catalytic activity
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 / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Non-ribosomal peptide synthase:Amino acid adenylation
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIzore, T. / Ho, Y.T.C. / Kaczmarski, J.A. / Gavriilidou, A. / Chow, K.H. / Steer, D. / Goode, R.J.A. / Schittenhelm, R.B. / Tailhades, J. / Tosin, M. ...Izore, T. / Ho, Y.T.C. / Kaczmarski, J.A. / Gavriilidou, A. / Chow, K.H. / Steer, D. / Goode, R.J.A. / Schittenhelm, R.B. / Tailhades, J. / Tosin, M. / Challis, G.L. / Krenske, E.H. / Ziemert, N. / Jackson, C.J. / 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: Nat Commun / Year: 2021
Title: Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity.
Authors: Izore, T. / Candace Ho, Y.T. / Kaczmarski, J.A. / Gavriilidou, A. / Chow, K.H. / Steer, D.L. / Goode, R.J.A. / Schittenhelm, R.B. / Tailhades, J. / Tosin, M. / Challis, G.L. / Krenske, E.H. ...Authors: Izore, T. / Candace Ho, Y.T. / Kaczmarski, J.A. / Gavriilidou, A. / Chow, K.H. / Steer, D.L. / Goode, R.J.A. / Schittenhelm, R.B. / Tailhades, J. / Tosin, M. / Challis, G.L. / Krenske, E.H. / Ziemert, N. / Jackson, C.J. / Cryle, M.J.
History
DepositionNov 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 2.0Apr 21, 2021Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2Apr 3, 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

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)115,4924
Polymers114,7762
Non-polymers7172
Water8,125451
1
A: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7462
Polymers57,3881
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7462
Polymers57,3881
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.501, 106.059, 106.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 57387.809 Da / Num. of mol.: 2 / Mutation: R2577G
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-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
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: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→47.68 Å / Num. obs: 81488 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.06 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 6.8 % / Num. unique obs: 4414 / CC1/2: 0.525 / Rpim(I) all: 0.65 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from SAD

Resolution: 2→47.68 Å / SU ML: 0.2249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 4172 5.13 %
Rwork0.1937 77194 -
obs0.1953 81366 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.25 Å2
Refinement stepCycle: LAST / Resolution: 2→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7921 0 0 451 8372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00458143
X-RAY DIFFRACTIONf_angle_d0.803411155
X-RAY DIFFRACTIONf_chiral_restr0.0471300
X-RAY DIFFRACTIONf_plane_restr0.0061487
X-RAY DIFFRACTIONf_dihedral_angle_d20.80131164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.3434990.29182548X-RAY DIFFRACTION99.77
2.02-2.050.32391180.28212546X-RAY DIFFRACTION99.78
2.05-2.070.3041320.26752555X-RAY DIFFRACTION99.74
2.07-2.10.29261030.26472566X-RAY DIFFRACTION99.89
2.1-2.130.31231430.26152538X-RAY DIFFRACTION99.74
2.13-2.150.30871530.25652533X-RAY DIFFRACTION99.93
2.15-2.190.31511350.24292559X-RAY DIFFRACTION99.93
2.19-2.220.26221210.23852547X-RAY DIFFRACTION99.93
2.22-2.250.28481620.23312534X-RAY DIFFRACTION99.96
2.25-2.290.25881560.22432506X-RAY DIFFRACTION99.96
2.29-2.330.22721170.2212592X-RAY DIFFRACTION99.93
2.33-2.370.26611650.21852528X-RAY DIFFRACTION99.93
2.37-2.420.27411690.21642544X-RAY DIFFRACTION99.96
2.42-2.470.2481410.2132534X-RAY DIFFRACTION99.93
2.47-2.520.25581800.20642522X-RAY DIFFRACTION99.96
2.52-2.580.23591550.20942533X-RAY DIFFRACTION100
2.58-2.640.24481500.20982549X-RAY DIFFRACTION100
2.64-2.710.25452110.20232500X-RAY DIFFRACTION99.96
2.71-2.790.2711220.2112585X-RAY DIFFRACTION99.96
2.79-2.880.26741070.2052606X-RAY DIFFRACTION99.93
2.88-2.990.29251660.19752522X-RAY DIFFRACTION99.96
2.99-3.110.20621110.20132615X-RAY DIFFRACTION99.96
3.11-3.250.21721140.18992616X-RAY DIFFRACTION99.89
3.25-3.420.19311230.18732606X-RAY DIFFRACTION100
3.42-3.630.18821530.18122563X-RAY DIFFRACTION100
3.63-3.910.2076880.17442665X-RAY DIFFRACTION100
3.91-4.310.19631400.16112618X-RAY DIFFRACTION99.96
4.31-4.930.1991350.1612625X-RAY DIFFRACTION100
4.93-6.210.1931600.19272660X-RAY DIFFRACTION100
6.21-47.680.1931430.17852779X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: -13.5448350198 Å / Origin y: 4.75760637426 Å / Origin z: 31.7976646809 Å
111213212223313233
T0.330016911396 Å20.0165336624308 Å2-0.01965469047 Å2-0.305448459257 Å2-0.0324515336933 Å2--0.30007165913 Å2
L0.701315306131 °20.181769355568 °2-0.0965500149383 °2-0.0600410805185 °2-0.0931922809258 °2---0.0156110034378 °2
S-0.0160676396216 Å °0.042210374127 Å °-0.0670747439056 Å °0.0105488694617 Å °0.00324794723142 Å °-0.0354296965179 Å °0.000517189801883 Å °-0.0107135466369 Å °-4.1471280043E-6 Å °
Refinement TLS groupSelection details: all

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