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- PDB-6no2: ADP bound to K114bD mutant ATP-grasp fold of Blastocystis hominis... -

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Basic information

Entry
Database: PDB / ID: 6no2
TitleADP bound to K114bD mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase
ComponentsSuccinate--CoA ligase [ADP-forming] subunit beta
KeywordsLIGASE / Complex / Mutant
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
ADENOSINE-5'-DIPHOSPHATE / Succinate--CoA ligase [ADP-forming] subunit beta
Similarity search - Component
Biological speciesBlastocystis sp. subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.159 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1327
Polymers55,1942
Non-polymers9385
Water1,74797
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-40 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.021, 77.748, 77.112
Angle α, β, γ (deg.)90.000, 125.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))
21(chain B and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))A2 - 59
121(chain A and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))A69 - 123
131(chain A and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))A132 - 233
211(chain B and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))B2 - 59
221(chain B and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))B69 - 123
231(chain B and (resid 2 through 59 or resid 69 through 123 or resid 132 through 233))B132 - 233

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Components

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


Mass: 27596.965 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253 / Mutation: 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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 12% w/v PEG3350, 100 mM MES, pH 5.3, 225 mM ammonium tartrate, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.159→54.56 Å / Num. obs: 29604 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.53 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.16-2.2230.592199.8
9.66-54.563.20.041199.2

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 2.159→54.544 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 27.53
RfactorNum. reflection% reflection
Rfree0.251 1428 4.82 %
Rwork0.2216 --
obs0.2231 29596 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.4 Å2 / Biso mean: 58.8993 Å2 / Biso min: 19.38 Å2
Refinement stepCycle: final / Resolution: 2.159→54.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 87 97 3690
Biso mean--83.46 37.69 -
Num. residues----456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2058X-RAY DIFFRACTION4.05TORSIONAL
12B2058X-RAY DIFFRACTION4.05TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1589-2.23610.29611230.27512802292599
2.2361-2.32560.29561480.260927722920100
2.3256-2.43150.32481480.249828292977100
2.4315-2.55970.30861380.249628092947100
2.5597-2.720.25471350.240727962931100
2.72-2.93010.28251520.2372793294599
2.9301-3.22490.26521470.222428262973100
3.2249-3.69140.23181530.220628142967100
3.6914-4.65050.24671340.191728432977100
4.6505-54.5610.2081500.209228843034100
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)
10.835-0.1269-0.55690.345-0.05060.46540.0279-0.07410.27360.01870.0706-0.0556-0.1610.031300.3054-0.0257-0.00060.2911-0.06210.3083-4.457910.727312.6725
20.52650.31080.23660.67320.30940.6201-0.0237-0.1214-0.04140.14160.0058-0.2263-0.0524-0.0244-00.3096-0.0413-0.04750.2934-0.00580.27813.67435.26634.4822
30.60110.4088-0.37150.5828-0.04330.3705-0.07860.068-0.241-0.02110.0744-0.1910.1667-0.0164-0.00060.2863-0.0460.0340.2456-0.02910.3217-8.9986-18.64669.4777
40.97830.02780.77440.71390.34490.77250.0546-0.0752-0.0983-0.0869-0.09410.17530.0021-0.1984-00.2694-0.05660.00980.2798-0.05410.3058-31.5712-13.0493.6607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:115)A1 - 115
2X-RAY DIFFRACTION2(chain A and resid 116:233)A116 - 233
3X-RAY DIFFRACTION3(chain B and resid 1:116)B1 - 116
4X-RAY DIFFRACTION4(chain B and resid 117:233)B117 - 233

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