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- PDB-6no6: K46bE&K114bD mutant ATP-grasp fold of Blastocystis hominis succin... -

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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 complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / magnesium ion binding / mitochondrion / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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