[English] 日本語
Yorodumi
- PDB-1e9l: The crystal structure of novel mammalian lectin Ym1 suggests a sa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e9l
TitleThe crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site
ComponentsYM1 SECRETORY PROTEIN
KeywordsMACROPHAGE SECRETORY PROTEIN / INFLAMMATION / LECTIN / INDUCIBLE / SECRETORY
Function / homology
Function and homology information


rough endoplasmic reticulum lumen / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / chitin catabolic process / chitin binding / polysaccharide catabolic process / nuclear envelope / carbohydrate binding / cytoplasmic vesicle ...rough endoplasmic reticulum lumen / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / : / chitin catabolic process / chitin binding / polysaccharide catabolic process / nuclear envelope / carbohydrate binding / cytoplasmic vesicle / inflammatory response / extracellular region / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases ...Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-amino-2-deoxy-beta-D-glucopyranose / Chitinase-like protein 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å
AuthorsHsiao, C.D. / Sun, Y.J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The Crystal Structure of a Novel Mammalian Lectin, Ym1, Suggests a Saccharide Binding Site
Authors: Sun, Y.J. / Chang, N.C. / Hung, S.I. / Chang, A.C. / Chou, C.C. / Hsiao, C.D.
History
DepositionOct 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / pdbx_database_proc ...atom_site / pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 1, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: chem_comp / pdbx_database_status ...chem_comp / pdbx_database_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _chem_comp.type / _pdbx_database_status.status_code_sf
Revision 2.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Oct 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 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "A" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "A" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YM1 SECRETORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5452
Polymers42,3661
Non-polymers1791
Water3,855214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.340, 60.660, 60.760
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein YM1 SECRETORY PROTEIN


Mass: 42365.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ORAL INFECTIONS OF MICE WITH TRICHINELLA SPIRALIS INDUCE PERITONEAL EXUDATE CELLS TO SECRETE YM1
Source: (natural) MUS MUSCULUS (house mouse) / Cell: PERITONEAL EXUDATE CELLS(MACROPHAGES) / Cellular location: CYTOPLASM / Strain: ICR / References: UniProt: O35744
#2: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 394-398 WERE NOT VISIBLE IN THE ELECTRON DENSITY. HOWEVER, AS THERE IS NO EVIDENCE TO ...RESIDUES 394-398 WERE NOT VISIBLE IN THE ELECTRON DENSITY. HOWEVER, AS THERE IS NO EVIDENCE TO SUGGEST THAT THESE RESIDUES ARE NOT PRESENT IN THE SAMPLE THEY HAVE BEEN INCLUDED IN THE SEQRES RECORD.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 44 %
Crystal growpH: 6 / Details: pH 6.00
Crystal
*PLUS
Crystal grow
*PLUS
Method: microdialysis / Details: Change, N.C., (2001) J.Biol.Chem., 276, 17497.

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 11644 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 3.69 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.15 / % possible all: 89.4
Reflection
*PLUS
Num. obs: 12671 / % possible obs: 97.3 % / Num. measured all: 46811
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.201

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1154 9.9 %RANDOM
Rwork0.198 ---
obs0.198 11644 94.2 %-
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-3.5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 12 214 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.81.5
X-RAY DIFFRACTIONx_mcangle_it1.32
X-RAY DIFFRACTIONx_scbond_it1.342
X-RAY DIFFRACTIONx_scangle_it0.522.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 147 8.6 %
Rwork0.244 1568 -
obs--89.4 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

+
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