[English] 日本語
Yorodumi
- PDB-6no6: K46bE&K114bD mutant ATP-grasp fold of Blastocystis hominis succin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6no6
TitleK46bE&K114bD mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase
ComponentsSuccinate--CoA ligase [ADP-forming] subunit beta
KeywordsLIGASE / Double mutation
Function / homology
Function and homology information


hydrogenosome / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / magnesium ion binding / ATP binding
Similarity search - Function
Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Succinyl-CoA synthetase-like / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
Succinate--CoA ligase [ADP-forming] subunit beta
Similarity search - Component
Biological speciesBlastocystis sp. subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.911 Å
AuthorsHuang, J. / Fraser, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)222915-2013 Canada
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis.
Authors: Huang, J. / Nguyen, V.H. / Hamblin, K.A. / Maytum, R. / van der Giezen, M. / Fraser, M.E.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate--CoA ligase [ADP-forming] subunit beta
B: Succinate--CoA ligase [ADP-forming] subunit beta


Theoretical massNumber of molelcules
Total (without water)55,1942
Polymers55,1942
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-7 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.987, 97.543, 67.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 94 or resid 96...
21(chain B and (resid 1 through 94 or resid 96...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHR(chain A and (resid 1 through 94 or resid 96...AA1 - 941 - 94
12GLNGLNVALVAL(chain A and (resid 1 through 94 or resid 96...AA96 - 10996 - 109
13METMETPHEPHE(chain A and (resid 1 through 94 or resid 96...AA1 - 2331 - 233
14METMETPHEPHE(chain A and (resid 1 through 94 or resid 96...AA1 - 2331 - 233
15CYSCYSSERSER(chain A and (resid 1 through 94 or resid 96...AA131 - 138131 - 138
16VALVALILEILE(chain A and (resid 1 through 94 or resid 96...AA158 - 160158 - 160
17THRTHRPHEPHE(chain A and (resid 1 through 94 or resid 96...AA167 - 233167 - 233
21METMETTHRTHR(chain B and (resid 1 through 94 or resid 96...BB1 - 941 - 94
22GLNGLNVALVAL(chain B and (resid 1 through 94 or resid 96...BB96 - 10996 - 109
23METMETASPASP(chain B and (resid 1 through 94 or resid 96...BB1 - 2341 - 234
24METMETASPASP(chain B and (resid 1 through 94 or resid 96...BB1 - 2341 - 234
25CYSCYSSERSER(chain B and (resid 1 through 94 or resid 96...BB131 - 138131 - 138
26VALVALILEILE(chain B and (resid 1 through 94 or resid 96...BB158 - 160158 - 160
27THRTHRPHEPHE(chain B and (resid 1 through 94 or resid 96...BB167 - 233167 - 233

-
Components

#1: Protein Succinate--CoA ligase [ADP-forming] subunit beta / Succinyl-CoA synthetase beta chain / SCS-beta


Mass: 27596.898 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253 / Mutation: K46E, K114D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastocystis sp. subtype 1 (strain ATCC 50177 / NandII) (eukaryote)
Strain: ATCC 50177 / NandII / Gene: SCSb / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3FHP0, succinate-CoA ligase (ADP-forming)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 14% w/v PEG3350, 100 mM MES, pH 6.5, 160 mM ammonium tartrate, pH 8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→55.42 Å / Num. obs: 43137 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.91-1.966.41.4311100
8.54-55.425.60.033199.8

-
Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3318refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 1.911→52.312 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.92
RfactorNum. reflection% reflection
Rfree0.2099 2136 4.96 %
Rwork0.1809 --
obs0.1823 43063 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.48 Å2 / Biso mean: 62.6477 Å2 / Biso min: 27.46 Å2
Refinement stepCycle: final / Resolution: 1.911→52.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 0 156 3695
Biso mean---49.27 -
Num. residues----463
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1849X-RAY DIFFRACTION5.487TORSIONAL
12B1849X-RAY DIFFRACTION5.487TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9107-1.95520.341160.308726902806
1.9552-2.00410.3321360.276126992835
2.0041-2.05820.28231360.253626902826
2.0582-2.11880.25961550.229726892844
2.1188-2.18720.25781480.215326892837
2.1872-2.26540.25331450.209726872832
2.2654-2.35610.22031480.201926742822
2.3561-2.46330.22221380.197827192857
2.4633-2.59320.22061490.185127242873
2.5932-2.75560.19671410.183527102851
2.7556-2.96840.24971600.19427322892
2.9684-3.26710.2071390.187227302869
3.2671-3.73970.20471330.173727702903
3.7397-4.71110.18251460.141527912937
4.7111-52.33190.17881460.171829333079
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)
12.54350.34330.32621.0919-0.15081.18880.1794-0.04760.21920.0537-0.12680.21520.0691-0.3279-00.3441-0.04790.01250.3658-0.04170.379325.823134.6248-10.8597
21.1777-0.1526-1.36630.756-0.71231.83270.1678-0.5039-0.13110.0695-0.09190.0962-0.31780.06960.00060.4323-0.08410.01650.5148-0.0410.343330.864330.013610.9563
32.10090.4246-0.44191.87380.14210.77160.15620.1386-0.0279-0.0192-0.1394-0.2687-0.00950.178-00.32440.0279-0.00320.33320.00940.347455.70839.4272-15.2069
41.1912-0.3944-1.911-0.66510.3842.8107-0.14560.2791-0.42040.0829-0.1157-0.0080.1966-0.0988-0.03880.42470.03690.02170.4082-0.1710.432553.6423.6263-31.838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:117)A1 - 117
2X-RAY DIFFRACTION2(chain A and resid 118:233)A118 - 233
3X-RAY DIFFRACTION3(chain B and resid 1:109)B1 - 109
4X-RAY DIFFRACTION4(chain B and resid 110:234)B110 - 234

+
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