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- PDB-2w39: Glc(beta-1-3)Glc disaccharide in -1 and -2 sites of Laminarinase ... -

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Basic information

Entry
Database: PDB / ID: 2w39
TitleGlc(beta-1-3)Glc disaccharide in -1 and -2 sites of Laminarinase 16A from Phanerochaete chrysosporium
ComponentsPUTATIVE LAMINARINASE
KeywordsHYDROLASE / PHANEROCHAETE CHRYSOSPORIUM / WHITE ROT FUNGUS / GLYCOSYL HYDROLASE / GH7 / GH16 / LAM16A / LAMINARIN / FAMILY 16 / BETA-GLUCAN / BASIDIOMYCETE / BETA-GLUCANASE / PICHEA PASTORIS / LAMINARINASE / BETA SANDWICH / EXTRACELLULAR
Function / homology
Function and homology information


glucan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-laminaribiose / D-glucono-1,5-lactone / Putative laminarinase
Similarity search - Component
Biological speciesPHANEROCHAETE CHRYSOSPORIUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsVasur, J. / Kawai, R. / Andersson, E. / Igarashi, K. / Sandgren, M. / Samejima, M. / Stahlberg, J.
CitationJournal: FEBS J. / Year: 2009
Title: X-Ray Crystal Structures of Phanerochaete Chrysosporium Laminarinase 16A in Complex with Products from Lichenin and Laminarin Hydrolysis
Authors: Vasur, J. / Kawai, R. / Andersson, E. / Igarashi, K. / Sandgren, M. / Samejima, M. / Stahlberg, J.
History
DepositionNov 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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_alt_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _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_comp_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 2.1Dec 13, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING SHEET RECORDS FOR CHAIN ID `A` HAVE ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING SHEET RECORDS FOR CHAIN ID `A` HAVE BEEN GENERATED BY BETA-SPIDER, VERSION ALPHA 2.0 WITH AN ENERGY THRESHOLD OF -8.2 KCAL/MOL USING COULOMB ELECTROSTATICS USING 12-6 L-J VAN DER WAALS USING BETA-SPIDER RULE SETS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE LAMINARINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6644
Polymers31,9231
Non-polymers7423
Water7,855436
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.147, 46.713, 152.550
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 PUTATIVE LAMINARINASE / LAMINARINASE 16A


Mass: 31922.721 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHANEROCHAETE CHRYSOSPORIUM (fungus) / Strain: K-3 / Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: Q874E3, endo-1,3(4)-beta-glucanase
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-LGC / D-glucono-1,5-lactone / (3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE / GLUCONOLACTONE


Type: D-saccharide / Mass: 178.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-ACETYL GLUCOSAMINE (NAG): REMAINING AFTER DEGLYCOSYLATION AND COVALENTLY LINKED TO ASN43 CHAIN A

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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: 2.1 Å3/Da / Density % sol: 40.2 % / Description: NONE
Crystal growpH: 5
Details: 10 MG/ML LAMINARINASE 16A IN 25 % PEG 3350, 0.2 M AMMONIUM NITRATE AND 10 MM NAOAC PH 5, CO-CRYSTALIZED WITH 10 MM 4-O-BETA-D-GLUCOSYL-LAMINARIBIOSE (G4G3G) LIGAND FOR 6 MONTHS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2005
Details: DIAMOND (111), GE(220) SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.1→29.55 Å / Num. obs: 98347 / % possible obs: 88.3 % / Observed criterion σ(I): 1.9 / Redundancy: 3.84 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.43
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 2.83 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 50.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CL2

2cl2


Resolution: 1.1→29.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / σ(F): 1.1 / ESU R: 0.033 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.152 4912 5.08 %RANDOM
Rwork0.138 ---
obs0.138 93358 88 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.054 Å20 Å20 Å2
2--0.079 Å20 Å2
3----0.025 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 49 436 2732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212528
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9173497
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55624.919124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.42315315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6471511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022077
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21259
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21771
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9891.51590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55122581
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9553938
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7034.5916
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 149 -
Rwork0.233 3459 -
obs--44.55 %

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