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- PDB-2pyh: Azotobacter vinelandii Mannuronan C-5 epimerase AlgE4 A-module co... -

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Basic information

Entry
Database: PDB / ID: 2pyh
TitleAzotobacter vinelandii Mannuronan C-5 epimerase AlgE4 A-module complexed with mannuronan trisaccharide
ComponentsPoly(beta-D-mannuronate) C5 epimerase 4
KeywordsISOMERASE / beta-helix / epimerase / mannuronic acid
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 / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Mannuronan C5-epimerase AlgE4
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsRozeboom, H.J. / Bjerkan, T.M. / Kalk, K.H. / Ertesvag, H. / Holtan, S. / Aachman, F.L. / Valla, S. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.
Authors: Rozeboom, H.J. / Bjerkan, T.M. / Kalk, K.H. / Ertesvag, H. / Holtan, S. / Aachmann, F.L. / Valla, S. / Dijkstra, B.W.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 24, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: Poly(beta-D-mannuronate) C5 epimerase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,67310
Polymers79,8462
Non-polymers8278
Water1,09961
1
A: Poly(beta-D-mannuronate) C5 epimerase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0434
Polymers39,9231
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(beta-D-mannuronate) C5 epimerase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6306
Polymers39,9231
Non-polymers7075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.551, 121.790, 45.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-404-

CA

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Components

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


Mass: 39923.180 Da / Num. of mol.: 2 / Fragment: A-module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: algE4 / Plasmid: pTB26 derivative of pTYB5 (NEB) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q44493, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Polysaccharide alpha-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAa1-4DManpAa1-4DManpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122A-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6-1.7 M Malonate, pH 7.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER PROTEUM R / Detector: CCD / Date: Oct 23, 2003 / Details: Montel200 multilayer graded optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→57.4 Å / Num. all: 26719 / Num. obs: 26719 / % possible obs: 99.2 % / Biso Wilson estimate: 65.9 Å2 / Rsym value: 0.107 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 1.9 / Num. unique all: 2699 / Rsym value: 0.561 / % possible all: 93.8

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
XPREPdata reduction
CNSphasing
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: native from other entry

Resolution: 2.7→57.4 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1336 5 %random
Rwork0.233 ---
all-26462 --
obs-26462 99.2 %-
Solvent computationBsol: 41.323 Å2
Displacement parametersBiso mean: 49.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.699 Å20 Å20 Å2
2--14.49 Å20 Å2
3----18.189 Å2
Refinement stepCycle: LAST / Resolution: 2.7→57.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 44 61 5709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.341
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramman.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbo1.param

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