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- PDB-3afl: Crystal structure of exotype alginate lyase Atu3025 H531A complex... -

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Basic information

Entry
Database: PDB / ID: 3afl
TitleCrystal structure of exotype alginate lyase Atu3025 H531A complexed with alginate trisaccharide
ComponentsOligo alginate lyase
KeywordsLYASE / ALPHA/ALPHA BALLEL / ANTI-PARALLEL BETA SHEET
Function / homology
Function and homology information


dermatan sulfate metabolic process / chondroitin-glucuronate 5-epimerase activity / chondroitin sulfate metabolic process / lyase activity / membrane
Similarity search - Function
Oligosaccharide lyase / : / Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 ...Oligosaccharide lyase / : / Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Oligo alginate lyase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsOchiai, A. / Yamasaki, M. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of exotype alginate lyase Atu3025 from Agrobacterium tumefaciens
Authors: Ochiai, A. / Yamasaki, M. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionMar 9, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 25, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligo alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4332
Polymers87,9051
Non-polymers5281
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.845, 99.643, 109.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Oligo alginate lyase / EXOTYPE ALGINATE LYASE


Mass: 87904.883 Da / Num. of mol.: 1 / Mutation: H531A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_L_3558, Atu3025 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: A9CEJ9, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 17% PEG 4000, 8.5% iso-propanol, 0.085M HEPES-Na, 15% glycerol, 10mM alginate trisaccharide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2009
RadiationMonochromator: Si(111) double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 18590 / % possible obs: 99.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.2
Reflection shellResolution: 2.99→3.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A0O

3a0o


Resolution: 2.99→37.85 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.87 / SU B: 19.764 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26234 943 5.1 %RANDOM
Rwork0.19888 ---
obs0.20211 17479 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.671 Å2
Baniso -1Baniso -2Baniso -3
1--3.36 Å20 Å20 Å2
2--6.5 Å20 Å2
3----3.14 Å2
Refinement stepCycle: LAST / Resolution: 2.99→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6149 0 36 62 6247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216399
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9398738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08823.313329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30515943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0651547
X-RAY DIFFRACTIONr_chiral_restr0.0750.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025093
X-RAY DIFFRACTIONr_nbd_refined0.2090.23079
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.23
X-RAY DIFFRACTIONr_mcbond_it0.3471.53887
X-RAY DIFFRACTIONr_mcangle_it0.63726167
X-RAY DIFFRACTIONr_scbond_it0.73432877
X-RAY DIFFRACTIONr_scangle_it1.2844.52571
LS refinement shellResolution: 2.992→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 65 -
Rwork0.289 1221 -
obs--94.56 %

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