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- PDB-2wne: Mutant Laminarinase 16A cyclizes laminariheptaose -

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Basic information

Entry
Database: PDB / ID: 2wne
TitleMutant Laminarinase 16A cyclizes laminariheptaose
ComponentsPUTATIVE LAMINARINASE
KeywordsHYDROLASE / LAMINARIN / FAMILY 16 / CYCLICAL POYSACCHARIDES / GLYCOSYL HYDROLASE / BETA SANDWICH / BASIDIOMYCETE / BETA-GLUCANASE / 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: 2.124 Å
AuthorsVasur, J. / Kawai, R. / Andersson, E. / Widmalm, G. / Jonsson, K.H.M. / Hansson, H. / Engstrom, A. / Einarsson, E. / Forsberg, Z. / Igarashi, K. ...Vasur, J. / Kawai, R. / Andersson, E. / Widmalm, G. / Jonsson, K.H.M. / Hansson, H. / Engstrom, A. / Einarsson, E. / Forsberg, Z. / Igarashi, K. / Sandgren, M. / Samejima, M. / Stahlberg, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Synthesis of Cyclic Beta-Glucan Using Laminarinase 16A Glycosynthase Mutant from the Basidiomycete Phanerochaete Chrysosporium.
Authors: Vasur, J. / Kawai, R. / Jonsson, K.H.M. / Widmalm, G. / Engstrom, A. / Frank, M. / Andersson, E. / Hansson, H. / Forsberg, Z. / Igarashi, K. / Samejima, M. / Sandgren, M. / Stahlberg, J.
History
DepositionJul 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Jul 12, 2017Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag ..._diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED. SECONDARY STRUCTURE ASSIGNED BY DSSP DSSP OUTPUT ... HELIX DETERMINATION METHOD: AUTHOR PROVIDED. SECONDARY STRUCTURE ASSIGNED BY DSSP DSSP OUTPUT CONVERTED BY DSSP2PDB VERSION 0.03
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING SHEET RECORDS FOR MODEL `1` CHAIN ID ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE FOLLOWING SHEET RECORDS FOR MODEL `1` CHAIN ID `A` HAVE BEEN DETERMINED 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)34,2693
Polymers31,8811
Non-polymers2,3882
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.175, 47.911, 152.766
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: 31880.686 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-318 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: NUCLEOPHILE MUTANT / Source: (gene. exp.) PHANEROCHAETE CHRYSOSPORIUM (fungus) / Strain: K-3 / Plasmid: PPICZALPHAA / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: Q874E3, EC: 3.2.1.6
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2-2-2/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1_f3-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 135 TO SER
Nonpolymer detailsALFA-LAMINARIHEPTAOSYL FLUORIDE (A401-A407): BETA-1-3-LINKED GLUCAN WITH AN ALPHA-FLUORIDE FOUND IN ...ALFA-LAMINARIHEPTAOSYL FLUORIDE (A401-A407): BETA-1-3-LINKED GLUCAN WITH AN ALPHA-FLUORIDE FOUND IN LAMINARIA DIGITATA. BETA-D-MANNOSE (BMA): PART OF N-GLYCOSYLATION ALPHA-GLYCOSYL-FLUORIDE (GLF): A402 HAS BETA-1,3 GLYCOSIDIC BOND TO THIS RESIDUE IN THE -1 SUBSITE. ALPHA-D-MANNOSE (MAN): PART OF N-GLYCOSYLATION BETA-D-GLUCOSE (BGC): BETA-1,3-GLUCAN IN THE ACTIVE SITE, WITH A407 AT +1 SUBSITE, A406 AT +2 AND A403 AT -3 AND A402 AT -2. B402 IS LINKED TO GLF WITH A BETA-1-3-GLYCOSIDIC BOND. N-ACETYL-D-GLUCOSAMINE (NAG): PART OF N-GLYCOSYLATION
Sequence detailsPOINT MUTATION OF NUCLEOPHILE RESIDUE GLUTAMATE 115 TO SERINE (THIS IS A E115S MUTANT)

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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 growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP: 1 UL 2MG/ML PROTEIN MIXED WITH 1 UL RESERVOIR SOLUTION: 20% PEG 3350, 0.2 M NH4NO3 PH 5 (REERVOIR VOLUME 500 UL). XTALS WERE SOAKED O/N IN DROP OF 10 MM AL7F AND EQUAL VOLUME ...Details: HANGING DROP: 1 UL 2MG/ML PROTEIN MIXED WITH 1 UL RESERVOIR SOLUTION: 20% PEG 3350, 0.2 M NH4NO3 PH 5 (REERVOIR VOLUME 500 UL). XTALS WERE SOAKED O/N IN DROP OF 10 MM AL7F AND EQUAL VOLUME 35% PEG, 0.2 M NH4NO3 PH 5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH / Detector: CCD / Date: May 16, 2008 / Details: MULTILAYER MIRROR
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 2.11→50.9 Å / Num. obs: 16720 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5 / % possible all: 81

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Processing

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

Resolution: 2.124→40.589 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.555 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 2.124 / ESU R: 0.261 / ESU R Free: 0.199 / Stereochemistry target values: RESTRAINED / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 820 5.08 %RANDOM
Rwork0.1598 ---
obs0.163 16341 98.839 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.021 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å20 Å20 Å2
2--0.015 Å20 Å2
3----0.009 Å2
Refinement stepCycle: LAST / Resolution: 2.124→40.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 161 263 2668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212515
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9763477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4524.609115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62715299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5781511
X-RAY DIFFRACTIONr_chiral_restr0.10.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021910
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21164
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21709
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6351.51528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08422409
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73231125
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5944.51068
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: 2.124→2.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 46 -
Rwork0.182 1041 -
obs--91.115 %

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