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- PDB-2ml1: Solution Structure of AlgE6R1 subunit from the Azotobacter vinela... -

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Basic information

Entry
Database: PDB / ID: 2ml1
TitleSolution Structure of AlgE6R1 subunit from the Azotobacter vinelandii Mannuronan C5-epimerase
ComponentsPoly(beta-D-mannuronate) C5 epimerase 6
KeywordsISOMERASE / Alginate C-5 epimerase / mannuronan C-5 epimerase / R-module
Function / homology
Function and homology information


mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / calcium ion binding / extracellular space
Similarity search - Function
: / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Right handed beta helix domain / Right handed beta helix region / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Hemolysin-type calcium-binding conserved site ...: / Peptidase M10 serralysin, C-terminal / Peptidase M10 serralysin C terminal / Right handed beta helix domain / Right handed beta helix region / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Carbohydrate-binding/sugar hydrolysis domain / 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 AlgE6
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBuchinger, E. / Wimmer, R. / Aachmann, F.L.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Structural and Functional Characterization of the R-modules in Alginate C-5 Epimerases AlgE4 and AlgE6 from Azotobacter vinelandii
Authors: Buchinger, E. / Knudsen, D.H. / Behrens, M.A. / Pedersen, J.S. / Aarstad, O.A. / Tndervik, A. / Valla, S. / Skjak-Brk, G. / Wimmer, R. / Aachmann, F.L.
#1: Journal: Biomol.Nmr Assign. / Year: 2008
Title: 1H, 15N, 13C resonance assignment of the AlgE6R1 subunit from the Azotobacter vinelandii mannuronan C5-epimerase
Authors: Aachmann, F.L. / Skjak-Braek, G.
History
DepositionFeb 18, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7047
Polymers15,4641
Non-polymers2406
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 6 / Mannuronan epimerase 6


Mass: 15463.654 Da / Num. of mol.: 1 / Fragment: UNP residues 382-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: algE6 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q9ZFH0, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the first R-module of AlgE6 from Azotobacter vinelandii
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HN(CO)CA
1713D HN(CA)CO
1813D HNCA
1913D HBHA(CO)NH
11023D (H)CCH-COSY
11123D (H)CCH-TOCSY
11213D 1H-15N NOESY
11322D 1H-1H NOESY
11423D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9-1.3 mM [U-98% 13C; U-98% 15N] AlgE6R1-1, 25 mM Calcium-2, 20 mM HEPES-3, 90% H2O/10% D2O90% H2O/10% D2O
20.9-1.3 mM [U-98% 13C; U-98% 15N] AlgE6R1-4, 25 mM Calcium-5, 20 mM HEPES-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMAlgE6R1-1[U-98% 13C; U-98% 15N]0.9-1.31
25 mMCalcium-21
20 mMHEPES-31
mMAlgE6R1-4[U-98% 13C; U-98% 15N]0.9-1.32
25 mMCalcium-52
20 mMHEPES-62
Sample conditionsIonic strength: 0.165 / pH: 6.9 / Pressure: 1 atm / 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
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
CARAKeller and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
YASARA11.11.2YASARA_Biosciencesrefinement
CYANAKrieger E, Koraimann G, Vriend Grefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3554 / NOE intraresidue total count: 2181 / NOE long range total count: 479 / NOE medium range total count: 112 / NOE sequential total count: 782 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 50
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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