[English] 日本語
Yorodumi
- PDB-7stu: Crystal structure of sulfatase from Pedobacter yulinensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7stu
TitleCrystal structure of sulfatase from Pedobacter yulinensis
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE
Function / homologySulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / hydrolase activity / BROMIDE ION / N-acetylgalactosamine-6-sulfatase
Function and homology information
Biological speciesPedobacter yulinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsO'Malley, A. / Schlachter, C.R. / Grimes, L.L. / Tomashek, J.J. / Lee, A.L. / Chruszcz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Molecules / Year: 2021
Title: Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis .
Authors: Schlachter, C.R. / O'Malley, A. / Grimes, L.L. / Tomashek, J.J. / Chruszcz, M. / Lee, L.A.
History
DepositionNov 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,90110
Polymers51,3921
Non-polymers5099
Water5,693316
1
A: N-acetylgalactosamine-6-sulfatase
hetero molecules

A: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,80220
Polymers102,7852
Non-polymers1,01718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)83.286, 83.286, 115.793
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-846-

HOH

-
Components

#1: Protein N-acetylgalactosamine-6-sulfatase /


Mass: 51392.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter yulinensis (bacteria) / Gene: C7T94_09545 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T3HKC0
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.15 M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000

-
Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→40 Å / Num. obs: 23149 / % possible obs: 99.2 % / Redundancy: 9.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.057 / Rrim(I) all: 0.172 / Rsym value: 0.128 / Net I/σ(I): 15.14
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 2 / Num. unique obs: 1144 / CC1/2: 0.738 / CC star: 0.922 / Rpim(I) all: 0.339 / Rrim(I) all: 0.858 / Rsym value: 0.907 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7STT

7stt


Resolution: 2.23→39.217 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.177 / SU ML: 0.164 / Cross valid method: FREE R-VALUE / ESU R: 0.302 / ESU R Free: 0.215
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2252 1205 5.235 %
Rwork0.1738 21815 -
all0.176 --
obs-23020 99.19 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 33.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20.565 Å20 Å2
2--1.13 Å2-0 Å2
3----3.664 Å2
Refinement stepCycle: LAST / Resolution: 2.23→39.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 9 316 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133586
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153292
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.654862
X-RAY DIFFRACTIONr_angle_other_deg1.3311.5837583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4335444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01422.335197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4415576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5441523
X-RAY DIFFRACTIONr_chiral_restr0.0640.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02868
X-RAY DIFFRACTIONr_nbd_refined0.2090.2811
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23191
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21758
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2307
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2480.223
X-RAY DIFFRACTIONr_nbd_other0.1960.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2360.21
X-RAY DIFFRACTIONr_mcbond_it1.0422.4861779
X-RAY DIFFRACTIONr_mcbond_other1.0392.4851778
X-RAY DIFFRACTIONr_mcangle_it1.8313.7262222
X-RAY DIFFRACTIONr_mcangle_other1.8313.7282223
X-RAY DIFFRACTIONr_scbond_it1.1052.581807
X-RAY DIFFRACTIONr_scbond_other1.1052.5811808
X-RAY DIFFRACTIONr_scangle_it1.9013.8112640
X-RAY DIFFRACTIONr_scangle_other1.9013.8112640
X-RAY DIFFRACTIONr_lrange_it6.2930.6024299
X-RAY DIFFRACTIONr_lrange_other6.13430.0584245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.2880.3191020.2821553X-RAY DIFFRACTION99.3397
2.288-2.350.308780.2181560X-RAY DIFFRACTION99.7564
2.35-2.4180.226810.1951523X-RAY DIFFRACTION99.442
2.418-2.4920.2511010.1721440X-RAY DIFFRACTION99.8704
2.492-2.5740.22660.1751424X-RAY DIFFRACTION98.6755
2.574-2.6640.186740.1641375X-RAY DIFFRACTION99.8622
2.664-2.7640.204770.1711348X-RAY DIFFRACTION99.7899
2.764-2.8760.238770.1681269X-RAY DIFFRACTION100
2.876-3.0030.24790.1711234X-RAY DIFFRACTION99.9239
3.003-3.1490.249490.1811200X-RAY DIFFRACTION100
3.149-3.3180.242640.191145X-RAY DIFFRACTION100
3.318-3.5180.226610.1891042X-RAY DIFFRACTION98.6583
3.518-3.7590.25520.173986X-RAY DIFFRACTION96.9188
3.759-4.0570.209380.151940X-RAY DIFFRACTION97.1202
4.057-4.4390.197380.14860X-RAY DIFFRACTION97.1861
4.439-4.9560.233400.145800X-RAY DIFFRACTION98.476
4.956-5.7080.143300.167719X-RAY DIFFRACTION99.8667
5.708-6.9550.239350.164616X-RAY DIFFRACTION100
6.955-9.6910.193470.153461X-RAY DIFFRACTION97.6923
9.691-39.2170.175150.193312X-RAY DIFFRACTION99.6951
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.59280.0821-0.12890.47380.08210.53640.02740.0725-0.10760.0271-0.0351-0.01930.0679-0.04290.00780.0948-0.0163-0.01840.1043-0.02530.0241-27.022418.689619.3851
23.11670.66021.13570.91140.0231.0701-0.02110.0511-0.37390.0115-0.0762-0.33010.04740.01260.09730.14460.0199-0.03090.1274-0.00740.2025-6.450414.171616.48
31.40970.71960.70830.77430.37910.9707-0.01770.13950.0267-0.0748-0.0224-0.01750.0239-0.07180.04010.0925-0.00530.00010.1647-0.00620.0058-24.793627.3529.676
41.1359-0.0284-0.02880.7650.01810.65490.09210.0470.1336-0.0052-0.0473-0.0804-0.097-0.0151-0.04480.08780.00470.00580.09490.01960.0285-19.757343.949418.0476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 209
2X-RAY DIFFRACTION2ALLA210 - 260
3X-RAY DIFFRACTION3ALLA261 - 344
4X-RAY DIFFRACTION4ALLA345 - 445

+
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