[English] 日本語
Yorodumi
- PDB-2wlq: Nucleophile-disabled Lam16A mutant holds laminariheptaose (L7) in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wlq
TitleNucleophile-disabled Lam16A mutant holds laminariheptaose (L7) in a cyclical conformation
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVasur, J. / Kawai, R. / Andersson, E. / Widmalm, G. / Jonsson, K.H. / Hansson, H. / Engstrom, A. / 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. / Widmalm, G. / Engstrom, A. / Frank, M. / Andersson, E. / Hansson, H. / Forsberg, Z. / Igarashi, K. / Samejima, M. / Sandgren, M. / Stahlberg, J.
History
DepositionJun 24, 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 / Refinement description / Version format compliance
Revision 1.2Jul 12, 2017Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms ...diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 8, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 3.0Jul 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_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 3.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE LAMINARINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2693
Polymers31,8811
Non-polymers2,3882
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.273, 47.910, 152.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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
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 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-(1-3)-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)-beta-D-glucopyranose


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


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 135 TO SER
Nonpolymer detailsLAMINARIHEPTAOSE, A BETA-1-3-LINKED GLUCAN FROM LAMINARIA DIGITATA, HAS BEEN ASSIGNED CHAIN B.
Sequence detailsPOINT MUTATION OF NUCLEOPHILE RESIDUE GLUTAMATE 115 TO SERINE (THIS IS A E115S MUTANT)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40 %
Description: RIGID BODY REFINEMENT WITH LAM16A APO STRUCTURE PDB 2CL2 AS MODEL
Crystal growTemperature: 293 K / pH: 5
Details: 8 MG/ML PROTEIN SOLUTION IN 10 MM NAOAC WAS MIXED WITH AN EQUAL VOLUME OF CRYSTALLIZATION BUFFER CONTAINING 20% PEG 3350, 0.2 M AMMONIUM NITRATE AND 10 MM SODIUM ACETATE BUFFER, PH 5.0, AT ...Details: 8 MG/ML PROTEIN SOLUTION IN 10 MM NAOAC WAS MIXED WITH AN EQUAL VOLUME OF CRYSTALLIZATION BUFFER CONTAINING 20% PEG 3350, 0.2 M AMMONIUM NITRATE AND 10 MM SODIUM ACETATE BUFFER, PH 5.0, AT 20 DEGREES. SOAKING: 24 H IN 5 MM LAMINAROHEPTASACCHARIDE. CRYOPROTECTANT CONTAINED 35 % (W/V) PEG 3350, 0.2 M AMMONIUM NITRATE AND 10 MM SODIUM ACETATE BUFFER, PH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.983
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 13, 2006 / Details: COLLIMATOR AND FOCUSING MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.4→23.8 Å / Num. obs: 56288 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 99.2

-
Processing

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

2cl2


Resolution: 1.4→23.843 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: RESTRAINED / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2851 5.16 %RANDOM
Rwork0.1696 ---
obs0.171 56165 99.781 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.998 Å2
Refinement stepCycle: LAST / Resolution: 1.4→23.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 161 363 2768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9953554
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48624.609115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451511
X-RAY DIFFRACTIONr_chiral_restr0.1450.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021922
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21192
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21819
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8421.51502
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48222420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96531062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.954.51134
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: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 227 -
Rwork0.221 3791 -
obs--98.24 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more