[English] 日本語
Yorodumi
- PDB-5o8l: Crystal structure of Leuconostoc citreum NRRL B-1299 N-terminally... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o8l
TitleCrystal structure of Leuconostoc citreum NRRL B-1299 N-terminally truncated dextransucrase DSR-M in complex with sucrose
ComponentsAlternansucrase
KeywordsTRANSFERASE / dextransucrase / dextran
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
sucrose / dextransucrase
Similarity search - Component
Biological speciesLeuconostoc citreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsClaverie, M. / Cioci, G. / Remaud-simeon, M. / Moulis, C. / Tranier, S.
CitationJournal: Acs Catalysis / Year: 2017
Title: Investigations on the Determinants Responsible for Low Molar Mass Dextran Formation by DSR-M Dextransucrase
Authors: Claverie, M. / Cioci, G. / Vuillemin, M. / Monties, N. / Roblin, P. / Lippens, G. / Remaud-Simeon, M. / Moulis, C.
History
DepositionJun 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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_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_conn_angle / 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.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alternansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3593
Polymers143,9761
Non-polymers3822
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-10 kcal/mol
Surface area43450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.625, 183.625, 146.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Alternansucrase


Mass: 143976.469 Da / Num. of mol.: 1 / Mutation: inactive mutant E715Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leuconostoc citreum (bacteria) / Gene: asr / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4A2Q1*PLUS, EC: 2.4.1.140
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.96 Å3/Da / Density % sol: 75.21 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane 6.5 20 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 32876 / % possible obs: 98.4 % / Redundancy: 3.9 % / Net I/σ(I): 4.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.907 / SU B: 58.849 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1608 4.9 %RANDOM
Rwork0.19849 ---
obs0.19996 31258 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.249 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å2-1.29 Å20 Å2
2---2.58 Å2-0 Å2
3---8.38 Å2
Refinement stepCycle: 1 / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8588 0 24 0 8612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028799
X-RAY DIFFRACTIONr_bond_other_d0.0010.027892
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.93411967
X-RAY DIFFRACTIONr_angle_other_deg0.747318141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38951096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86325.588451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.551151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6781530
X-RAY DIFFRACTIONr_chiral_restr0.0670.21300
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022114
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.176.2844388
X-RAY DIFFRACTIONr_mcbond_other2.176.2844387
X-RAY DIFFRACTIONr_mcangle_it3.5319.435480
X-RAY DIFFRACTIONr_mcangle_other3.539.4315481
X-RAY DIFFRACTIONr_scbond_it2.4316.4694411
X-RAY DIFFRACTIONr_scbond_other2.436.4694411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9839.6246488
X-RAY DIFFRACTIONr_long_range_B_refined5.55550.70110191
X-RAY DIFFRACTIONr_long_range_B_other5.55450.70410192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 107 -
Rwork0.285 2297 -
obs--98.93 %
Refinement TLS params.Method: refined / Origin x: -46.1364 Å / Origin y: 56.7677 Å / Origin z: -6.439 Å
111213212223313233
T0.11 Å2-0.0654 Å20.0221 Å2-0.138 Å2-0.0244 Å2--0.2192 Å2
L0.4416 °20.2457 °20.1366 °2-2.0831 °21.1211 °2--0.7873 °2
S-0.0238 Å °0.202 Å °-0.0688 Å °-0.3155 Å °0.1531 Å °-0.3884 Å °-0.1619 Å °0.097 Å °-0.1293 Å °

+
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