[English] 日本語
Yorodumi
- PDB-6dey: Aspartylglucosaminuria mutant structure and function -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dey
TitleAspartylglucosaminuria mutant structure and function
Components
  • Glycosylasparaginase, residues 188-331
  • Glycosylasparaginase, residues 38-178
KeywordsHYDROLASE
Function / homology
Function and homology information


(Glycosyl)asparaginase / Peptidase T2, asparaginase 2 / Asparaginase / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycosylasparaginase
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 Å
AuthorsPande, S. / Laksminarasimhan, D. / Guo, H.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)DK075294 United States
CitationJournal: FEBS Lett. / Year: 2018
Title: Biochemical and structural insights into an allelic variant causing the lysosomal storage disorder - aspartylglucosaminuria.
Authors: Pande, S. / Bizilj, W. / Guo, H.C.
History
DepositionMay 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosylasparaginase, residues 38-178
B: Glycosylasparaginase, residues 188-331
C: Glycosylasparaginase, residues 38-178
D: Glycosylasparaginase, residues 188-331


Theoretical massNumber of molelcules
Total (without water)62,1514
Polymers62,1514
Non-polymers00
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-97 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.980, 96.560, 61.750
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glycosylasparaginase, residues 38-178


Mass: 15684.853 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: BMF97_04835 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1V3U2Z4
#2: Protein Glycosylasparaginase, residues 188-331


Mass: 15390.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: BMF97_04835 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1V3U2Z4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 100mM Tri, pH 7.5, 50 mM NaCl, 10 mM EDTA

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.63→61.8 Å / Num. obs: 68901 / % possible obs: 97.3 % / Redundancy: 3.7 % / Net I/σ(I): 0
Reflection shellResolution: 1.6→1.641 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.63→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.347 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19739 3358 5.1 %RANDOM
Rwork0.16873 ---
obs0.17019 65359 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0.15 Å2
2--0.61 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 0 222 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194383
X-RAY DIFFRACTIONr_bond_other_d0.0020.024157
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.9515903
X-RAY DIFFRACTIONr_angle_other_deg1.1439644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3724.74192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48715784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8771526
X-RAY DIFFRACTIONr_chiral_restr0.1470.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024904
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02850
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_it1.3551.1492260
X-RAY DIFFRACTIONr_mcbond_other1.3381.1482259
X-RAY DIFFRACTIONr_mcangle_it1.8871.722818
X-RAY DIFFRACTIONr_mcangle_other1.8871.7212819
X-RAY DIFFRACTIONr_scbond_it2.6541.5062123
X-RAY DIFFRACTIONr_scbond_other2.6541.5082124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8942.1223086
X-RAY DIFFRACTIONr_long_range_B_refined4.67614.7144909
X-RAY DIFFRACTIONr_long_range_B_other4.65914.5994881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 255 -
Rwork0.169 4660 -
obs--94.34 %

+
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://pdbjlvh1.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