[English] 日本語
Yorodumi
- PDB-6y0k: Sulfite oxidase from Thermus thermophilus with coordinated phosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y0k
TitleSulfite oxidase from Thermus thermophilus with coordinated phosphate
ComponentsPutaitve sulfite oxidase
KeywordsOXIDOREDUCTASE / Molybdoenzyme / Sulfite Oxidase
Function / homology
Function and homology information


sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / heme binding
Similarity search - Function
Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set
Similarity search - Domain/homology
(MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM / PHOSPHATE ION / Putaitve sulfite oxidase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDjeghader, A. / Soulimane, T.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase.
Authors: Djeghader, A. / Rossotti, M. / Abdulkarim, S. / Biaso, F. / Gerbaud, G. / Nitschke, W. / Schoepp-Cothenet, B. / Soulimane, T. / Grimaldi, S.
History
DepositionFeb 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Putaitve sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,41010
Polymers43,1561
Non-polymers1,2549
Water7,530418
1
AAA: Putaitve sulfite oxidase
hetero molecules

AAA: Putaitve sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,81920
Polymers86,3122
Non-polymers2,50718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area9000 Å2
ΔGint-101 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.600, 130.600, 114.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11AAA-675-

HOH

21AAA-768-

HOH

31AAA-820-

HOH

41AAA-823-

HOH

51AAA-837-

HOH

61AAA-852-

HOH

71AAA-909-

HOH

-
Components

#1: Protein Putaitve sulfite oxidase


Mass: 43156.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: TTHA1325 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): TP1000 / References: UniProt: Q5SIP4
#2: Chemical ChemComp-MSS / (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM


Mass: 505.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12MoN5O7PS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.8 Na/K phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96851 Å / Relative weight: 1
ReflectionResolution: 1.7→42.75 Å / Num. obs: 63544 / % possible obs: 99.94 % / Redundancy: 13.6 % / Biso Wilson estimate: 25.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08164 / Rpim(I) all: 0.02249 / Net I/σ(I): 18.68
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 14 % / Rmerge(I) obs: 1.063 / Mean I/σ(I) obs: 2.67 / Num. unique obs: 6247 / CC1/2: 0.826 / Rpim(I) all: 0.2857 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BLF

2blf


Resolution: 1.7→42.749 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.702 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1909 2000 3.147 %
Rwork0.1658 --
all0.167 --
obs-63543 99.967 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 26.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.345 Å20.172 Å20 Å2
2--0.345 Å2-0 Å2
3----1.119 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 70 418 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133149
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172902
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6614302
X-RAY DIFFRACTIONr_angle_other_deg1.3331.5736736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48421.598169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41415495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531525
X-RAY DIFFRACTIONr_chiral_restr0.0730.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023522
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02676
X-RAY DIFFRACTIONr_nbd_refined0.2710.21035
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.22761
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21486
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2910.270
X-RAY DIFFRACTIONr_nbd_other0.310.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.26
X-RAY DIFFRACTIONr_mcbond_it1.5712.5771521
X-RAY DIFFRACTIONr_mcbond_other1.5682.5751520
X-RAY DIFFRACTIONr_mcangle_it2.2043.8591903
X-RAY DIFFRACTIONr_mcangle_other2.2053.8611904
X-RAY DIFFRACTIONr_scbond_it2.7422.8941627
X-RAY DIFFRACTIONr_scbond_other2.7412.8961628
X-RAY DIFFRACTIONr_scangle_it4.1454.2162392
X-RAY DIFFRACTIONr_scangle_other4.1444.2182393
X-RAY DIFFRACTIONr_lrange_it6.21632.9753825
X-RAY DIFFRACTIONr_lrange_other6.21632.993826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.2781450.26144600.26146050.8760.8811000.249
1.744-1.7920.2361420.22643830.22745250.9040.9131000.213
1.792-1.8440.2471370.20942230.2143600.9110.9241000.188
1.844-1.90.2191350.19141280.19242630.9360.941000.169
1.9-1.9620.1851300.18140040.18241340.9470.9451000.157
1.962-2.0310.2121260.17638820.17740080.9290.9431000.153
2.031-2.1080.191220.16337540.16438770.9550.96199.97420.142
2.108-2.1940.1811180.15636170.15637350.9570.9631000.136
2.194-2.2910.2031130.15234830.15435960.9520.9621000.134
2.291-2.4020.1981070.1533160.15134230.9540.9661000.132
2.402-2.5320.1911030.1531720.15132750.9620.9671000.135
2.532-2.6850.185990.15430100.15531090.9550.9661000.141
2.685-2.8690.188920.16328380.16429360.9440.95899.79560.154
2.869-3.0980.192860.16326690.16427550.9640.9661000.159
3.098-3.3920.189800.17224450.17225260.960.96799.96040.172
3.392-3.7890.157730.15322470.15323210.9750.97599.95690.159
3.789-4.370.164640.13719970.13820610.9720.9771000.153
4.37-5.3380.159560.14117000.14217570.9760.9899.94310.162
5.338-7.4910.195450.1913720.1914180.9750.96999.92950.214
7.491-42.7490.293270.2298430.238720.930.94599.77060.28

+
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