[English] 日本語
Yorodumi
- PDB-2ydq: CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ydq
TitleCpOGA D298N in complex with hOGA-derived O-GlcNAc peptide
Components
  • BIFUNCTIONAL PROTEIN NCOAT
  • O-GLCNACASE NAGJ
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein O-linked glycosylation / protein deglycosylation ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / glycoprotein catabolic process / protein O-GlcNAcase / : / : / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein O-linked glycosylation / protein deglycosylation / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate binding / carbohydrate metabolic process / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
: / Hyaluronidase post-catalytic domain-like / Hyaluronidase post-catalytic domain-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 ...: / Hyaluronidase post-catalytic domain-like / Hyaluronidase post-catalytic domain-like / Cellulosome anchoring protein, cohesin domain / Cohesin domain / Glycosyl hydrolases family 84 (GH84) domain profile. / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / CBM2/CBM3, carbohydrate-binding domain superfamily / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Acyl-CoA N-acyltransferase / Fibronectin type III domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Protein O-GlcNAcase / O-GlcNAcase NagJ
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsSchimpl, M. / Borodkin, V.S. / Gray, L.J. / van Aalten, D.M.F.
CitationJournal: Chem.Biol. / Year: 2012
Title: Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition.
Authors: Schimpl, M. / Borodkin, V.S. / Gray, L.J. / Van Aalten, D.M.F.
History
DepositionMar 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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_auth_seq_id / _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.pdbx_role / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" 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: O-GLCNACASE NAGJ
T: BIFUNCTIONAL PROTEIN NCOAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,15822
Polymers66,8012
Non-polymers2,35720
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area29660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.210, 118.210, 148.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein O-GLCNACASE NAGJ / O-GLCNACASE / CPNAGJ / BETA-N-ACETYLHEXOSAMINIDASE / GH84 / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...O-GLCNACASE / CPNAGJ / BETA-N-ACETYLHEXOSAMINIDASE / GH84 / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDASE


Mass: 66130.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 31-618 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PGEX6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q0TR53, beta-N-acetylhexosaminidase
#2: Protein/peptide BIFUNCTIONAL PROTEIN NCOAT / / MENINGIOMA-EXPRESSED ANTIGEN 5 / NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE / PROTEIN O- ...MENINGIOMA-EXPRESSED ANTIGEN 5 / NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE / PROTEIN O-GLCNACASE / GLYCOSIDE HYDROLASE O-GLCNACASE / HEXOSAMINIDASE C / N-ACETYL-BETA-D-GLUCOSAMINIDASE / N-ACETYL-BETA-GLUCOSAMINIDASE / O-GLCNACASE / OGA


Mass: 670.758 Da / Num. of mol.: 1 / Fragment: HOGA O-GLCNAC PEPTIDE, RESIDUES 402-408 / Source method: obtained synthetically / Details: O-GLCNAC GLYCOSYLATION ON S405 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O60502, protein O-GlcNAcase
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cd
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 298 TO ASN ENGINEERED RESIDUE IN CHAIN A, ASN 388 TO ASP

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.6M NAAC, 0.175M CDSO4, 0.1M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 36085 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 36.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→24.7 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.392 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23053 735 2 %RANDOM
Rwork0.19302 ---
obs0.19376 35251 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.199 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 33 104 4753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9536406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13425.909242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31815789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.121518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213656
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5991.52910
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25224684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07431809
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6554.51722
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_free15.674319
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 51 -
Rwork0.268 2568 -
obs--99.47 %

+
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