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- PDB-2w52: 2 beta-glucans (6-O-glucosyl-laminaritriose) in both donor and ac... -

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Basic information

Entry
Database: PDB / ID: 2w52
Title2 beta-glucans (6-O-glucosyl-laminaritriose) in both donor and acceptor sites of GH16 Laminarinase 16A from Phanerochaete chrysosporium.
ComponentsPUTATIVE LAMINARINASE
KeywordsHYDROLASE / LAMINARIN / FAMILY 16 / EXTRACELLULAR / BETA SANDWICH / BASIDIOMYCETE / BETA- GLUCANASE / GLYCOSYL HYDROLASE / 3/1 / GH7 / GH16 / LAM16A / BETA-1\ / 6-GLUCAN
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
Putative laminarinase
Similarity search - Component
Biological speciesPHANEROCHAETE CHRYSOSPORIUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.56 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
DepositionDec 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING HELIX RECORDS HAVE BEEN GENERATED BY ... HELIX DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING HELIX RECORDS HAVE BEEN GENERATED BY BETA-SPIDER, VERSION ALPHA 2.0.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING SHEET RECORDS HAVE BEEN GENERATED BY ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING SHEET RECORDS 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)34,3294
Polymers31,9231
Non-polymers2,4063
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.056, 46.690, 152.871
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 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-6)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-6DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b3-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(6+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details6-O-GLUCOSYL-LAMINARITRIOSE: GLCP-BETA-1-6-GLCP-BETA-1-3- GLCP-BETA1-3-GLCP, A.K.A. G6G3G3G FROM ...6-O-GLUCOSYL-LAMINARITRIOSE: GLCP-BETA-1-6-GLCP-BETA-1-3- GLCP-BETA1-3-GLCP, A.K.A. G6G3G3G FROM LAMINARIA DIGITATA. BETA-D-MANNOSE (BMA): PART OF N-GLYCOSYLATION BETA GLUCOSE (BGC): ACCEPTOR-SITE G6G3G3 LIGAND COMPRISED OF A401, A402, A403, A404. DONOR LIGAND A405, A406, A407, NO BETA-1-6 GLUCOSE BRANCH DETECTED N-ACETYL-D-GLUCOSAMINE (NAG): PART OF N-GLYCOSYLATION

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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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 5
Details: 45 MG/ML LAM16A CRYSTALIZED IN 20% PEG 3350, 0.2 M AMMONIUM NITRATE AND 10 MM NAOAC PH 5, THEN SOAKED WITH 10 MM LIGAND FOR 90 MIN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.041
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 1.55→34.42 Å / Num. obs: 39543 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.3
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 5.78 / % possible all: 81.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.56→34.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.181 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 1.562 / ESU R: 0.08 / ESU R Free: 0.075 / Stereochemistry target values: RESTRAINED / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1981 5.09 %RANDOM
Rwork0.151 ---
obs0.152 39468 99.5 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.071 Å20 Å2
3----0.041 Å2
Refinement stepCycle: LAST / Resolution: 1.56→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 162 422 2831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9713493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98524.53117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68115305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9371512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021931
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21266
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21772
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2337
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7961.51534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28822427
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.90431137
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7334.51063
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: 1.562→1.602 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 144 -
Rwork0.196 2560 -
obs--94.51 %

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