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- PDB-1urx: Crystallographic structure of beta-agarase A in complex with olig... -

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Basic information

Entry
Database: PDB / ID: 1urx
TitleCrystallographic structure of beta-agarase A in complex with oligoagarose
ComponentsBETA-AGARASE A
KeywordsHYDROLASE / BETA-AGARASE / AGAROSE / GLYCOSIDE HYDROLASE / FAMILY 16 / DOUBLE HELIX / TWO BINDING-SITES
Function / homology
Function and homology information


beta-agarase / beta-agarase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Beta-agarase/YXIM esterase-like, galactose-binding domain-like / Beta-agarase / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily ...: / Beta-agarase/YXIM esterase-like, galactose-binding domain-like / Beta-agarase / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-agarase A / Beta-agarase A
Similarity search - Component
Biological speciesZOBELLIA GALACTANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllouch, J. / Helbert, W. / Henrissat, B. / Czjzek, M.
CitationJournal: Structure / Year: 2004
Title: Parallel Substrate Binding Sites in a Beta-Agarase Suggest a Novel Mode of Action on Double-Helical Agarose
Authors: Allouch, J. / Helbert, W. / Henrissat, B. / Czjzek, M.
History
DepositionNov 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_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_asym_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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-AGARASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8874
Polymers32,1351
Non-polymers1,7523
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.380, 51.380, 205.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein BETA-AGARASE A


Mass: 32135.389 Da / Num. of mol.: 1 / Fragment: BETA-AGARASE A DOMAIN, RESIDUES 20-290 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TWO MOLECULES OF OLIGOAGAROSE / Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9RGX9, UniProt: G0L322*PLUS, beta-agarase
#2: Polysaccharide 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L- ...3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 630.548 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2112h-1a_1-5][a1221h-1a_1-5_3-6][a2112h-1b_1-5]/1-2-3-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][<C12O9>]{[(1+1)][b-D-Galp]{[(3+1)]{}}}LINUCSPDB-CARE
#3: Polysaccharide 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L- ...3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose


Type: oligosaccharide / Mass: 1080.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,7,6/[a1221h-1a_1-5_3-6][a2112h-1b_1-5]/1-2-1-2-1-2-1/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1WURCSPDB2Glycan 1.1.0
[][<C30O21>]{[(1+1)][b-D-Galp]{[(3+1)]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, GLU 147 TO SER 147

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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: 2.81 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293.65 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30 % PEG 4000 200 MM AMMONIUM ACETATE, 100 MM SODIUM ACETATE PH 4.6
Crystal grow
*PLUS
Temperature: 20.5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13.5 mg/mlprotein1drop
250 mMTris1droppH7.5
325 mM1dropNaCl
44 mMagaro-octaose1drop
530 %PEG40001reservoir
6200 mMammonium acetate1reservoir
7100 mMsodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→37.2 Å / Num. obs: 34045 / % possible obs: 95.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.8 / % possible all: 98.4
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 37.2 Å / Redundancy: 4.4 % / Num. measured all: 148960 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.8

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O4Y

1o4y


Resolution: 1.7→37.2 Å / SU B: 1.641 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.18249 1709 5 %RANDOM
Rwork0.15503 ---
obs0.15642 32273 95.07 %-
Displacement parametersBiso mean: 13.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 117 354 2623
Refinement
*PLUS
Num. reflection obs: 32767 / % reflection Rfree: 5 % / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.762

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