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- PDB-7kw3: Non Ribosomal PCP domain -

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Basic information

Entry
Database: PDB / ID: 7kw3
TitleNon Ribosomal PCP domain
ComponentsPCP domain
KeywordsBIOSYNTHETIC PROTEIN / NRPS / PCP-domain
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / 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. / AMP-dependent synthetase/ligase ...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 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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
Non-ribosomal peptide synthase:Amino acid adenylation
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / chem_comp / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conf / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.label_seq_id ..._atom_site.auth_seq_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _audit_author.name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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 / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _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_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_seq_id
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 2.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PCP domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4652
Polymers9,3691
Non-polymers961
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area4580 Å2
Unit cell
Length a, b, c (Å)100.914, 100.914, 100.914
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Symmetry operation#1: x,y,z
#2: x+3/4,-z+3/4,y+1/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+3/4,y+1/4,x+3/4
#6: -y+3/4,x+1/4,z+3/4
#7: y+3/4,-x+3/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+3/4,-y+3/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+3/4,z+1/4,y+3/4
#24: -x+1/4,-z+1/4,-y+1/4
Components on special symmetry positions
IDModelComponents
11A-3701-

SO4

21A-3817-

HOH

31A-3826-

HOH

41A-3831-

HOH

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Components

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


Mass: 9368.553 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: BIS-TRIS, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→45.13 Å / Num. obs: 8284 / % possible obs: 100 % / Redundancy: 40.9 % / Biso Wilson estimate: 47.81 Å2 / CC1/2: 1 / Rpim(I) all: 0.03 / Net I/σ(I): 24.3
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 780 / CC1/2: 0.734 / Rpim(I) all: 0.39

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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 iTasser

Resolution: 2.3→45.13 Å / SU ML: 0.3063 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 394 4.78 %
Rwork0.1842 7854 -
obs0.1852 8248 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms573 0 5 56 634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059588
X-RAY DIFFRACTIONf_angle_d0.8222803
X-RAY DIFFRACTIONf_chiral_restr0.045195
X-RAY DIFFRACTIONf_plane_restr0.0062104
X-RAY DIFFRACTIONf_dihedral_angle_d26.8622200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.29191430.2532511X-RAY DIFFRACTION99.77
2.64-3.320.24681190.21182589X-RAY DIFFRACTION99.93
3.32-45.130.1751320.16162754X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.3549647145 Å / Origin y: 0.0827273954356 Å / Origin z: -0.291748690697 Å
111213212223313233
T0.369130796251 Å20.0337736692255 Å20.0383507086658 Å2-0.341189508826 Å2-0.00127689053466 Å2--0.336819737005 Å2
L4.83445087529 °2-0.608218584268 °2-1.40172755377 °2-3.02425596648 °20.0259515471149 °2--6.63127162129 °2
S0.09199808259 Å °-0.0316284928796 Å °0.247553167294 Å °0.166204864962 Å °0.0545508557151 Å °0.10260641048 Å °-0.591894332899 Å °-0.063865006683 Å °0.00472657481424 Å °
Refinement TLS groupSelection details: all

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