[English] 日本語
Yorodumi
- PDB-1auk: HUMAN ARYLSULFATASE A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1auk
TitleHUMAN ARYLSULFATASE A
ComponentsARYLSULFATASE A
KeywordsHYDROLASE / CEREBROSIDE-3-SULFATE HYDROLYSIS / LYSOSOMAL ENZYME
Function / homology
Function and homology information


cerebroside-sulfatase / cerebroside-sulfatase activity / arylsulfatase activity / sulfuric ester hydrolase activity / glycosphingolipid metabolic process / lysosomal lumen / azurophil granule lumen / lysosome / endoplasmic reticulum lumen / neutrophil degranulation ...cerebroside-sulfatase / cerebroside-sulfatase activity / arylsulfatase activity / sulfuric ester hydrolase activity / glycosphingolipid metabolic process / lysosomal lumen / azurophil granule lumen / lysosome / endoplasmic reticulum lumen / neutrophil degranulation / calcium ion binding / extracellular exosome / extracellular region
Sulfatase, N-terminal / Alkaline-phosphatase-like, core domain superfamily / C-terminal region of aryl-sulfatase / Sulfatase / Sulfatase, conserved site / Arylsulfatase, C-terminal domain - #10 / Arylsulfatase, C-terminal domain / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / 2-Layer Sandwich ...Sulfatase, N-terminal / Alkaline-phosphatase-like, core domain superfamily / C-terminal region of aryl-sulfatase / Sulfatase / Sulfatase, conserved site / Arylsulfatase, C-terminal domain - #10 / Arylsulfatase, C-terminal domain / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Arylsulfatase A
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsLukatela, G. / Krauss, N. / Theis, K. / Gieselmann, V. / Von Figura, K. / Saenger, W.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of human arylsulfatase A: the aldehyde function and the metal ion at the active site suggest a novel mechanism for sulfate ester hydrolysis.
Authors: Lukatela, G. / Krauss, N. / Theis, K. / Selmer, T. / Gieselmann, V. / von Figura, K. / Saenger, W.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 29, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2012Group: Derived calculations

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ARYLSULFATASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4234
Polymers51,9571
Non-polymers4673
Water3,171176
1
A: ARYLSULFATASE A
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)419,38832
Polymers415,6548
Non-polymers3,73424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area22750 Å2
ΔGint-114 kcal/mol
Surface area122670 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)132.630, 132.630, 192.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein ARYLSULFATASE A / / CEREBROSIDE-3-SULFATE-SULFATASE


Mass: 51956.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: C-DNA EXPRESSION / Cellular location: LYSOSOME / Gene: ARSA / Organ: TESTISTesticle / Plasmid: PBEH
Cell line (production host): BABY HAMSTER KIDNEY CELLS (BHK)
Cellular location (production host): SECRETED ENZYME / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P15289, cerebroside-sulfatase
#2: Chemical ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#3: Sugar ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#4: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR ...Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000, vapor diffusion - hanging drop
PH range: 5.0-5.4
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMsodium acetate1reservoir
210-13 %PEG60001reservoir
3100 mMsodium acetate1drop
410-13 %PEG60001drop
51.25 %octyl-beta-glucopyranoside1drop
610 mMTris-HCl1drop
7150 mM1dropNaCl

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 49794 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 34.97 Å2 / Rsym value: 0.055 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.35 / % possible all: 98
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.276

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.1→30 Å / σ(F): 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2463 5 %SHELLS
Rwork0.232 ---
Obs0.248 49794 98.6 %-
Displacement parametersBiso mean: 43.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 29 176 3785
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.8
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 49794
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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