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- PDB-6th8: Reconstructing the Origins of the HemD-like fold -

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Basic information

Entry
Database: PDB / ID: 6th8
TitleReconstructing the Origins of the HemD-like fold
ComponentscU3Sd
KeywordsFLAVOPROTEIN / protein design / HemD-like fold / flavodoxin-like fold
Function / homology
Function and homology information


uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / protoporphyrinogen IX biosynthetic process
Similarity search - Function
Rossmann fold - #10090 / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase superfamily / Uroporphyrinogen-III synthase / Uroporphyrinogen-III synthase HemD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen-III synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsColes, M. / Toledo-Patino, S. / Chaubey, M. / Hocker, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council647548 Germany
CitationJournal: Biochemistry / Year: 2019
Title: Reconstructing the Remote Origins of a Fold Singleton from a Flavodoxin-Like Ancestor.
Authors: Toledo-Patino, S. / Chaubey, M. / Coles, M. / Hocker, B.
History
DepositionNov 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cU3Sd


Theoretical massNumber of molelcules
Total (without water)13,6521
Polymers13,6521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7680 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein cU3Sd


Mass: 13651.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P48246*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic23D HNCA
131isotropic13D H(CCO)NH
141isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution / Contents: 29 mM [U-13C; U-15N] cU3Sd, 90% H2O/10% D2O / Label: 15N,13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 29 mM / Component: cU3Sd / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 1 Not defined / Label: 1 / pH: 8 Not defined / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 21

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