[English] 日本語
Yorodumi
- PDB-1odz: Expansion of the glycosynthase repertoire to produce defined mann... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1odz
TitleExpansion of the glycosynthase repertoire to produce defined manno-oligosaccharides
ComponentsMannan endo-1,4-beta-mannosidase
KeywordsHYDROLASE / MANNANASE / FAMILY 26 / GLYCOSIDE-HYDROLASE / GLYCOSYNTHASE / MANNO-OLIGOSACCHARIDE
Function / homology
Function and homology information


glucomannan metabolic process / galactomannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Mannan endo-1,4-beta-mannosidase
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJahn, M. / Stoll, D. / Warren, R.A.J. / Szabo, L. / Singh, P. / Gilbert, H.J. / Ducros, V.M.A. / Davies, G.J. / Withers, S.G.
CitationJournal: Chem.Commun.(Camb.) / Year: 2003
Title: Expansion of the Glycosynthase Repertoire to Produce Defined Manno-Oligosaccharides
Authors: Jahn, M. / Stoll, D. / Warren, R.A.J. / Szabo, L. / Singh, P. / Gilbert, H.J. / Ducros, V.M.A. / Davies, G.J. / Withers, S.G.
History
DepositionMar 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.page_last / _entity.pdbx_description ..._citation.page_last / _entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type
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 / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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_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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannan endo-1,4-beta-mannosidase
B: Mannan endo-1,4-beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,45710
Polymers87,3512
Non-polymers1,1068
Water18,6091033
1
A: Mannan endo-1,4-beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2285
Polymers43,6761
Non-polymers5534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Mannan endo-1,4-beta-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2285
Polymers43,6761
Non-polymers5534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.855, 131.855, 54.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHRAA44 - 887 - 51
21PROPROTHRTHRBB44 - 887 - 51
12THRTHRVALVALAA90 - 42253 - 385
22THRTHRVALVALBB90 - 42253 - 385

NCS oper: (Code: given
Matrix: (-0.99926, 0.03833, -0.00157), (-0.03832, -0.99926, -0.00155), (-0.00163, -0.00149, 1)
Vector: 65.89867, 65.95024, 27.31247)

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Mannan endo-1,4-beta-mannosidase / Mannanase 26A / Man26A / Mannanase A / ManA


Mass: 43675.582 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-423 / Mutation: E320G
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH MANNOBIOSE / Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Gene: manA, man26A, CJA_2770 / Plasmid: PET21A / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P49424, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 1039 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1033 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED MUTATION: GLU (320) GLY
Sequence detailsRESIDUES 1-28 COMPRISE THE SIGNAL PEPTIDE. MATURE CRYSTALLISED FORM OF MAN26A E320G MUTANT CONSISTS ...RESIDUES 1-28 COMPRISE THE SIGNAL PEPTIDE. MATURE CRYSTALLISED FORM OF MAN26A E320G MUTANT CONSISTS OF RESIDUES MET-38 TO LYS-423.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5
Details: 100MM TRIS 7.5, 26% PEG550, 9MM ZNSO4, 10MM MANNOTETRAOSE, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. obs: 171242 / % possible obs: 93.7 % / Redundancy: 4.01 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 29.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.21 / % possible all: 64.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J9Y

1j9y


Resolution: 1.4→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.961 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 8545 5 %RANDOM
Rwork0.151 ---
obs0.152 162650 93.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6065 0 66 1033 7164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216337
X-RAY DIFFRACTIONr_bond_other_d0.0020.025464
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9258657
X-RAY DIFFRACTIONr_angle_other_deg1.279312682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027130
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021358
X-RAY DIFFRACTIONr_nbd_refined0.2180.21305
X-RAY DIFFRACTIONr_nbd_other0.2540.26568
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.23344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2651
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9521.53781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40126117
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93232556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8224.52540
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→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 446
Rwork0.253 8143

+
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://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