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- PDB-2agm: Solution structure of the R-module from AlgE4 -

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Basic information

Entry
Database: PDB / ID: 2agm
TitleSolution structure of the R-module from AlgE4
ComponentsPoly(beta-D-mannuronate) C5 epimerase 4
KeywordsISOMERASE / parallel beta-roll
Function / homology
Function and homology information


mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / calcium ion binding / extracellular region
Similarity search - Function
Right handed beta helix domain / Right handed beta helix region / Carbohydrate-binding/sugar hydrolysis domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) ...Right handed beta helix domain / Right handed beta helix region / Carbohydrate-binding/sugar hydrolysis domain / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Parallel beta-helix repeat / Parallel beta-helix repeats / Serralysin-like metalloprotease, C-terminal / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Mannuronan C5-epimerase AlgE4
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, torsion angle dynamics, energy-minimisation
AuthorsAachmann, F.L. / Svanem, B.I. / Guntert, P. / Petersen, S.B. / Valla, S. / Wimmer, R.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: NMR structure of the R-module: a parallel beta-roll subunit from an Azotobacter vinelandii mannuronan C-5 epimerase.
Authors: Aachmann, F.L. / Svanem, B.I. / Guntert, P. / Petersen, S.B. / Valla, S. / Wimmer, R.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 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
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(beta-D-mannuronate) C5 epimerase 4


Theoretical massNumber of molelcules
Total (without water)16,9761
Polymers16,9761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Poly(beta-D-mannuronate) C5 epimerase 4 / Mannuronan epimerase 4 / R-module


Mass: 16976.012 Da / Num. of mol.: 1 / Fragment: R-module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: R-module subunit from algE4 / Plasmid: pFA2 derivative of pTYB11 (NEB) / Production host: Escherichia coli (E. coli) / Strain (production host): ER 2566
References: UniProt: Q44493, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy and torsion angles estimates from secondary chemical shifts using TALOS

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Sample preparation

DetailsContents: 1.6mM R-module U-99% 13C; U-99% 15N, 50mM CaCl2, 20mM Na-HEPES(pH 6.9)
Solvent system: 5% D2O, 95% H2O
Sample conditionsIonic strength: 0.17 / pH: 6.9 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1.5GUENTERTstructure solution
XwinNMR2.6Brukerprocessing
XEASY1.1.13Bartelsdata analysis
TALOS98.040.21.02Cornilescudata analysis
OPALp1.4KORADI, R., BILLETER, M., GUNTERT, P.structure solution
OPALp1.4KORADI, R., BILLETER, M., GUNTERT, P.refinement
RefinementMethod: DISTANCE GEOMETRY, torsion angle dynamics, energy-minimisation
Software ordinal: 1
Details: The structures are based on a total of 1714 unique restraints, 1576 are NOE-derived distance constraints, 138 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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