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- PDB-2zab: Crystal Structure of Family 7 Alginate Lyase A1-II' Y284F in Cmpl... -

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Basic information

Entry
Database: PDB / ID: 2zab
TitleCrystal Structure of Family 7 Alginate Lyase A1-II' Y284F in Cmplex with Product (GGG)
ComponentsAlginate lyase
KeywordsLYASE / ALGINATE LYASE / POLYSACCHARIDE LYASE FAMILY 7 / Y284F / COMPLEX
Function / homology
Function and homology information


Alginate lyase 2 / Alginate lyase / Jelly Rolls - #200 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSphingomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsOgura, K. / Yamasaki, M. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: To be Published
Title: Substrate Recognition in Tunnel of Family 7 Alginate Lyase from Sphingomonas sp. A1
Authors: Ogura, K. / Yamasaki, M. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionOct 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4163
Polymers25,7771
Non-polymers6382
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.730, 68.102, 79.950
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: Protein Alginate lyase / Alginate lyase A1-II


Mass: 25777.496 Da / Num. of mol.: 1 / Fragment: residues 81-313 / Mutation: Y284F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. (bacteria) / Strain: A1 / Gene: aly / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q75WP3, mannuronate-specific alginate lyase
#2: Polysaccharide alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LGulpAa1-4LGulpAa1-4LGulpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1121A-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLGU 403 AND BEM 501 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 1.83 Å3/Da / Density % sol: 32.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 1000, 15% PEG 8000, 0.2M calcium acetate, 0.05M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING 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: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 22667 / % possible obs: 97.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 56.7
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.9 / Num. unique all: 10515 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CWS

2cws


Resolution: 1.66→31.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.819 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19379 1164 5.1 %RANDOM
Rwork0.15976 ---
obs0.16159 21461 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.66→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 54 274 2051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221892
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5882.0072593
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55525.44379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18115296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.984154
X-RAY DIFFRACTIONr_chiral_restr0.1050.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.2948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21316
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7211.51167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12921835
X-RAY DIFFRACTIONr_scbond_it1.8663832
X-RAY DIFFRACTIONr_scangle_it2.6574.5747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.657→1.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 77 -
Rwork0.204 1442 -
obs--90.9 %

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