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

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Basic information

Entry
Database: PDB / ID: 6vtz
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


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 / Chloramphenicol acetyltransferase-like domain superfamily ...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 / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesMethanobrevibacter ruminantium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 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


Theoretical massNumber of molelcules
Total (without water)56,4241
Polymers56,4241
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.920, 139.920, 71.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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 BL21 (bacteria) / References: UniProt: D3E027
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystals were grown by vapour diffusion, hanging drop method. Drop volume was 2 micro-litre (1+1) equilibrated against 500 micro-litre of reservoir volume containing 0.1 M MOPS/Na-HEPES ...Details: Crystals were grown by vapour diffusion, hanging drop method. Drop volume was 2 micro-litre (1+1) equilibrated against 500 micro-litre of reservoir volume containing 0.1 M MOPS/Na-HEPES buffer at pH 7.5, 15% PEG MME and 14% PEG 20K as precipitants in the presence of 0.02M each of L-Na Glutamate, DL-Alanine, Glycine, DL-Lysine HCl, DL-Serine as additives. The concentration of protein was 30 mg/ml in HEPES buffer at pH 7.5 containing 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.65→46.291 Å / Num. obs: 23800 / % possible obs: 99.9 % / Redundancy: 10.72 % / Biso Wilson estimate: 75.77 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.221 / Net I/σ(I): 7.07
Reflection shellResolution: 2.65→2.83 Å / Num. unique obs: 8693 / CC1/2: 0.338

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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: 2.65→46.291 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1137 4.78 %
Rwork0.2032 22653 -
obs0.2051 23790 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.02 Å2 / Biso mean: 73.5979 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.65→46.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 5 2970
Biso mean---73.11 -
Num. residues----374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.65-2.77060.33961350.32132798
2.7706-2.91670.31271640.28222800
2.9167-3.09940.29771440.25852778
3.0994-3.33860.2961580.23242811
3.3386-3.67450.26921450.20562795
3.6745-4.20580.22791320.17662849
4.2058-5.29770.20131400.17382842
5.2977-46.2910.23011190.19962980

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