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- PDB-2ml3: Solution Structure of AlgE6R3 subunit from the Azotobacter vinela... -

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Basic information

Entry
Database: PDB / ID: 2ml3
TitleSolution Structure of AlgE6R3 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: 2011
Title: NMR assignments of 1H, 13C and 15N resonances of the C-terminal subunit from Azotobacter vinelandii mannuronan C5-epimerase 6 (AlgE6R3)
Authors: Buchinger, E. / Skjak-Brk, G. / Valla, S. / Wimmer, R. / Aachmann, F.L.
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)18,4787
Polymers18,2371
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: 18237.443 Da / Num. of mol.: 1 / Fragment: UNP residues 695-874 / Mutation: A180T
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 third 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 HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D HN(CA)CO
11213D HNHAHB
11332D 1H-1H NOESY
11413D 1H-15N NOESY
11523D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.15 mM [U-13C; U-15N] AlgE6R3-1, 20 mM HEPES-2, 25 mM CaCl2-3, 90 % H20-4, 10 % D20-5, 90% H2O/10% D2O90% H2O/10% D2O
20.15 mM [U-13C; U-15N] AlgE6R3-6, 20 mM HEPES-7, 25 mM CaCl2-8, 100 % D20-9, 100% D2O100% D2O
30.15 mM [U-13C; U-15N] AlgE6R3-10, 20 mM [U-2H] HEPES-11, 25 mM CaCl2-12, 100 % D20-13, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.15 mMAlgE6R3-1[U-13C; U-15N]1
20 mMHEPES-21
25 mMCaCl2-31
90 %H20-41
10 %D20-51
0.15 mMAlgE6R3-6[U-13C; U-15N]2
20 mMHEPES-72
25 mMCaCl2-82
100 %D20-92
0.15 mMAlgE6R3-10[U-13C; U-15N]3
20 mMHEPES-11[U-2H]3
25 mMCaCl2-123
100 %D20-133
Sample conditionspH: 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
CARAKeller and Wuthrichchemical shift assignment
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
TopSpin1.3Krieger E, Koraimann G, Vriend Gchemical shift assignment
TopSpin1.3Krieger E, Koraimann G, Vriend Gcollection
TopSpin1.3Krieger E, Koraimann G, Vriend Grefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
YASARAYASARA Biosciencesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2146 / NOE intraresidue total count: 889 / NOE long range total count: 553 / NOE medium range total count: 98 / NOE sequential total count: 606 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 51 / Protein psi angle constraints total count: 51
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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