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- PDB-7kvw: Non-ribosomal didomain (holo-PCP-C) acceptor bound state -

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Basic information

Entry
Database: PDB / ID: 7kvw
TitleNon-ribosomal didomain (holo-PCP-C) 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
4'-PHOSPHOPANTETHEINE / Non-ribosomal peptide synthase:Amino acid adenylation
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_symm_contact / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _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 / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_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_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)115,6934
Polymers114,9762
Non-polymers7172
Water4,522251
1
A: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8462
Polymers57,4881
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PCP-C didomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8462
Polymers57,4881
Non-polymers3581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.550, 105.931, 108.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
1ens_1
2ens_1
3ens_1

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
21ens_1(chain "A" and (resid 2 through 2905 or resid 2907 through 2984 or resid 2986 through 2999))
31ens_1(chain "B" and (resid 1 through 2550 or resid 2557...

NCS oper: (Code: givenMatrix: (0.0984954961893, 0.00558886554717, -0.995121802501), (0.000846203298688, -0.999984338017, -0.00553241903336), (-0.995137136866, -0.000297156994055, -0.098498682871) ...NCS oper: (Code: given
Matrix: (0.0984954961893, 0.00558886554717, -0.995121802501), (0.000846203298688, -0.999984338017, -0.00553241903336), (-0.995137136866, -0.000297156994055, -0.098498682871)
Vector: -24.2609739245, 26.7996216665, -26.7128283641)

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Components

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


Mass: 57487.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: FscG, Tfu_1867 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47NR9
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


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


Mass: 18.015 Da / Num. of mol.: 251 / 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: 53.98 %
Crystal growTemperature: 293.15 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: 0.9374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9374 Å / Relative weight: 1
ReflectionResolution: 2.18→48.14 Å / Num. obs: 61896 / % possible obs: 97.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.42 Å2 / Net I/σ(I): 12.4
Reflection shellResolution: 2.18→2.23 Å / Mean I/σ(I) obs: 2.3 / % possible all: 93.4

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Processing

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

Resolution: 2.18→47.42 Å / SU ML: 0.255 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.148
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.227 3027 4.89 %
Rwork0.192 --
obs0.193 61839 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.97 Å2
Refinement stepCycle: LAST / Resolution: 2.18→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7966 0 0 251 8217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038175
X-RAY DIFFRACTIONf_angle_d0.68711195
X-RAY DIFFRACTIONf_dihedral_angle_d18.3262973
X-RAY DIFFRACTIONf_chiral_restr0.0441299
X-RAY DIFFRACTIONf_plane_restr0.0041494
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDTypeAuth asym-ID
ens_11X-RAY DIFFRACTIONPOSITIONAL
ens_12X-RAY DIFFRACTIONPOSITIONALA
ens_13X-RAY DIFFRACTIONPOSITIONALB
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.33111410.29582429X-RAY DIFFRACTION89
2.21-2.250.28691600.2592692X-RAY DIFFRACTION99
2.25-2.290.27241280.24882707X-RAY DIFFRACTION99
2.29-2.330.27221540.23592663X-RAY DIFFRACTION98
2.33-2.370.24741240.22542710X-RAY DIFFRACTION99
2.37-2.420.28131510.23182667X-RAY DIFFRACTION98
2.42-2.470.27621490.22212687X-RAY DIFFRACTION98
2.47-2.530.28391580.2172652X-RAY DIFFRACTION97
2.53-2.60.25861380.2112648X-RAY DIFFRACTION97
2.6-2.670.26151550.21642638X-RAY DIFFRACTION97
2.67-2.740.25461370.21152703X-RAY DIFFRACTION98
2.74-2.830.26351470.22022688X-RAY DIFFRACTION98
2.83-2.930.31291310.21892705X-RAY DIFFRACTION98
2.93-3.050.24391470.20792677X-RAY DIFFRACTION98
3.05-3.190.21171440.2092673X-RAY DIFFRACTION97
3.19-3.360.23111400.20012672X-RAY DIFFRACTION97
3.36-3.570.24891040.19142699X-RAY DIFFRACTION96
3.57-3.840.20271910.17012575X-RAY DIFFRACTION94
3.84-4.230.2166960.17232727X-RAY DIFFRACTION96
4.23-4.840.16451150.16052709X-RAY DIFFRACTION95
4.84-6.10.22271390.18752690X-RAY DIFFRACTION95
6.1-47.420.165780.16662801X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -21.2104 Å / Origin y: 13.1426 Å / Origin z: -5.0911 Å
111213212223313233
T0.3037 Å20.0285 Å20.0511 Å2-0.315 Å20.0389 Å2--0.2628 Å2
L0.2261 °20.2404 °20.1477 °2-0.7867 °20.1459 °2---0.0081 °2
S0.016 Å °0.0074 Å °0.0667 Å °0.0599 Å °-0.034 Å °0.0789 Å °-0.0075 Å °-0.0263 Å °0 Å °
Refinement TLS groupSelection details: ALL

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