[English] 日本語
Yorodumi
- PDB-2oym: Endo-glycoceramidase II from Rhodococcus sp.: five-membered imino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oym
TitleEndo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol complex
ComponentsEndoglycoceramidase II
KeywordsHYDROLASE / (alpha/beta)8 (TIM) barrel
Function / homology
Function and homology information


endoglycosylceramidase / endoglycosylceramidase activity / carbohydrate derivative catabolic process / polysaccharide catabolic process / lipid catabolic process
Similarity search - Function
Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Glycoside hydrolase family 5, C-terminal domain / Glycoside hydrolase family 5 C-terminal domain / : / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-MNI / Endoglycoceramidase II
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsCaines, M.E.C. / Strynadka, N.C.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: The structural basis of glycosidase inhibition by five-membered iminocyclitols: the clan a glycoside hydrolase endoglycoceramidase as a model system.
Authors: Caines, M.E. / Hancock, S.M. / Tarling, C.A. / Wrodnigg, T.M. / Stick, R.V. / Stutz, A.E. / Vasella, A. / Withers, S.G. / Strynadka, N.C.
History
DepositionFeb 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoglycoceramidase II
B: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9106
Polymers104,2452
Non-polymers6654
Water12,160675
1
A: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4553
Polymers52,1231
Non-polymers3322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglycoceramidase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4553
Polymers52,1231
Non-polymers3322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.786, 93.282, 94.471
Angle α, β, γ (deg.)90.000, 98.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 43 - 490 / Label seq-ID: 34 - 481

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Endoglycoceramidase II


Mass: 52122.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: M-777 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Tuner) / References: UniProt: O33853, endoglycosylceramidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MNI / N-{[(2R,3R,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PYRROLIDIN-2-YL]METHYL}-4-(DIMETHYLAMINO)BENZAMIDE / 1-(4-DIMETHYLAMINO)BENZOYLAMINO-1,2,5-TRIDEOXY-2,5-IMINO-D-MANNITOL


Mass: 309.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.841→18.3 Å / Num. obs: 72622 / % possible obs: 91.9 % / Redundancy: 4 % / Biso Wilson estimate: 21.22 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 14.1
Reflection shellResolution: 1.841→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / Num. measured all: 33486 / Num. unique all: 8650 / Rsym value: 0.346 / % possible all: 75.4

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OSW

2osw


Resolution: 1.86→18.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.99 / SU ML: 0.091 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3701 5.1 %RANDOM
Rwork0.18 ---
obs0.182 72620 93.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.128 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.16 Å2
2--0.46 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.86→18.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6773 0 46 675 7494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226932
X-RAY DIFFRACTIONr_bond_other_d0.0020.024576
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9589522
X-RAY DIFFRACTIONr_angle_other_deg0.894311077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67723.633311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03915956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8761548
X-RAY DIFFRACTIONr_chiral_restr0.0640.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021428
X-RAY DIFFRACTIONr_nbd_refined0.1910.21369
X-RAY DIFFRACTIONr_nbd_other0.1920.24918
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23357
X-RAY DIFFRACTIONr_nbtor_other0.0830.23352
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2540
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1490.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.215
X-RAY DIFFRACTIONr_mcbond_it0.4921.54358
X-RAY DIFFRACTIONr_mcbond_other0.1471.51754
X-RAY DIFFRACTIONr_mcangle_it0.8827015
X-RAY DIFFRACTIONr_scbond_it1.21932778
X-RAY DIFFRACTIONr_scangle_it1.924.52498
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5517 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.170.5
MEDIUM THERMAL0.912
LS refinement shellResolution: 1.86→1.905 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 225 -
Rwork0.258 4405 -
obs-4630 81.87 %

+
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