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- PDB-6vtj: Structure of a thiolation-reductase di-domain from an archaeal no... -

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Basic information

Entry
Database: PDB / ID: 6vtj
TitleStructure of a thiolation-reductase di-domain from an archaeal non-ribosomal peptide synthetase
ComponentsNon-ribosomal peptide synthetase
KeywordsOXIDOREDUCTASE / non-ribosomal peptide synthetases / peptide carrier protein / reductase domain
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / catalytic activity / phosphopantetheine binding / cytoplasm
Similarity search - Function
Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site ...Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesMethanobrevibacter ruminantium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDeshpande, S. / Lott, J.S. / Lee, T.V.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Ministry of Business, Innovation and Employment (New Zealand)UOAX1506 New Zealand
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural characterization of a PCP-R didomain from an archaeal nonribosomal peptide synthetase reveals novel interdomain interactions.
Authors: Deshpande, S. / Altermann, E. / Sarojini, V. / Lott, J.S. / Lee, T.V.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Refinement description
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_nonpoly_scheme / pdbx_struct_assembly / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _exptl_crystal_grow.pdbx_details / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_percent_reflns_obs / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_ls_shell.d_res_high / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7822
Polymers56,4241
Non-polymers3581
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.949, 71.833, 82.725
Angle α, β, γ (deg.)90.000, 90.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-ribosomal peptide synthetase


Mass: 56423.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1) (archaea)
Strain: ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1 / Gene: mru_0351 / Production host: Escherichia coli (E. coli) / References: UniProt: D3E027
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: Crystals were grown by vapor diffusion, sitting drop method. Drop volume was 2 micro-liter (1+1) equilibrated against 50 micro-liter of reservoir volume of 1.7 M malic acid at pH 6.1. The ...Details: Crystals were grown by vapor diffusion, sitting drop method. Drop volume was 2 micro-liter (1+1) equilibrated against 50 micro-liter of reservoir volume of 1.7 M malic acid at pH 6.1. The concentration of protein was 30 mg/ml in HEPES buffer at pH 7.5 containing 150 mM of NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.948→47.636 Å / Num. obs: 40262 / % possible obs: 92.4 % / Redundancy: 3.82 % / Biso Wilson estimate: 32.22 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.48
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 4098 / CC1/2: 0.126

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6C

4f6c


Resolution: 1.95→47.62 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1927 4.93 %
Rwork0.196 37128 -
obs0.198 39055 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.05 Å2 / Biso mean: 37.17 Å2 / Biso min: 21 Å2
Refinement stepCycle: final / Resolution: 1.95→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 18 248 3981
Biso mean--38.58 41.74 -
Num. residues----472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.99690.41231400.3759249287
1.9969-2.05090.34021380.3461245499
2.0509-2.11130.2425220.300440597
2.1113-2.17940.32821480.28672868100
2.1794-2.25730.29961400.28582852100
2.2573-2.34770.28961560.24882878100
2.3477-2.45450.28641410.23552889100
2.4545-2.58390.28361520.22752866100
2.5839-2.74580.26691660.22682856100
2.7458-2.95780.27971570.20712876100
2.9578-3.25540.261500.19362859100
3.2554-3.72630.24411230.16422926100
3.7263-4.69410.15421580.13152925100
4.6941-47.60.18231360.16772982100

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