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- PDB-6no3: ADP bound to V113bL mutant ATP-grasp fold of Blastocystis hominis... -

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Basic information

Entry
Database: PDB / ID: 6no3
TitleADP bound to V113bL 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 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
ADENOSINE-5'-DIPHOSPHATE / Succinate--CoA ligase [ADP-forming] subunit beta
Similarity search - Component
Biological speciesBlastocystis sp. subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.939 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 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2138
Polymers55,2502
Non-polymers9636
Water3,351186
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-54 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.380, 117.345, 127.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 25 or resid 30...
21(chain B and (resid 1 through 25 or resid 30...

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
11METMETALAALA(chain A and (resid 1 through 25 or resid 30...AA1 - 251 - 25
12ARGARGARGARG(chain A and (resid 1 through 25 or resid 30...AA3030
13ARGARGPROPRO(chain A and (resid 1 through 25 or resid 30...AA32 - 7732 - 77
14GLUGLUILEILE(chain A and (resid 1 through 25 or resid 30...AA79 - 10279 - 102
15CYSCYSVALVAL(chain A and (resid 1 through 25 or resid 30...AA104 - 107104 - 107
16VALVALILEILE(chain A and (resid 1 through 25 or resid 30...AA109 - 123109 - 123
17PROPROPROPRO(chain A and (resid 1 through 25 or resid 30...AA132 - 152132 - 152
18CYSCYSPHEPHE(chain A and (resid 1 through 25 or resid 30...AA154 - 156154 - 156
19VALVALILEILE(chain A and (resid 1 through 25 or resid 30...AA158 - 160158 - 160
110GLUGLULYSLYS(chain A and (resid 1 through 25 or resid 30...AA169 - 235169 - 235
21METMETALAALA(chain B and (resid 1 through 25 or resid 30...BB1 - 251 - 25
22ARGARGARGARG(chain B and (resid 1 through 25 or resid 30...BB3030
23ARGARGPROPRO(chain B and (resid 1 through 25 or resid 30...BB32 - 7732 - 77
24GLUGLUILEILE(chain B and (resid 1 through 25 or resid 30...BB79 - 10279 - 102
25METMETLYSLYS(chain B and (resid 1 through 25 or resid 30...BB1 - 2351 - 235
26VALVALMETMET(chain B and (resid 1 through 25 or resid 30...BB109 - 1109 - 1
27CYSCYSPHEPHE(chain B and (resid 1 through 25 or resid 30...BB154 - 156154 - 156
28VALVALILEILE(chain B and (resid 1 through 25 or resid 30...BB158 - 160158 - 160
29METMETLYSLYS(chain B and (resid 1 through 25 or resid 30...BB1 - 2351 - 235
210GLUGLULYSLYS(chain B and (resid 1 through 25 or resid 30...BB169 - 235169 - 235

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Components

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


Mass: 27625.084 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253 / Mutation: V113L
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


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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 10% w/v PEG3350, 100 mM MES, pH 6.0, 200 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: 1.939→63.95 Å / Num. obs: 51125 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.94-1.996.10.8731100
8.68-63.955.90.037199.9

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3318refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 1.939→63.918 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 27.59
RfactorNum. reflection% reflection
Rfree0.2166 2396 4.7 %
Rwork0.1937 --
obs0.1948 51002 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.88 Å2 / Biso mean: 69.8763 Å2 / Biso min: 33.18 Å2
Refinement stepCycle: final / Resolution: 1.939→63.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 88 186 3874
Biso mean--68.27 58.34 -
Num. residues----470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1984X-RAY DIFFRACTION1.273TORSIONAL
12B1984X-RAY DIFFRACTION1.273TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9392-1.97880.4981380.44452760289899
1.9788-2.02190.41151210.407228913012100
2.0219-2.06890.37461370.36112825296299
2.0689-2.12060.34561570.32462790294799
2.1206-2.1780.33371540.284528212975100
2.178-2.24210.28471410.247428252966100
2.2421-2.31440.24561320.227828472979100
2.3144-2.39720.22551380.208128482986100
2.3972-2.49310.20591500.20228152965100
2.4931-2.60660.22641380.178228502988100
2.6066-2.7440.21211380.169628693007100
2.744-2.9160.19181280.176128602988100
2.916-3.14110.21191450.195528683013100
3.1411-3.45720.20521400.18128773017100
3.4572-3.95740.18931500.170428923042100
3.9574-4.98560.15881440.147529223066100
4.9856-63.95270.22111450.188430463191100
Refinement TLS params.Method: refined / Origin x: -11.8698 Å / Origin y: 12.3613 Å / Origin z: 12.151 Å
111213212223313233
T0.4095 Å20.0122 Å20.0045 Å2-0.3925 Å2-0.042 Å2--0.4582 Å2
L2.4151 °20.219 °2-0.4568 °2-0.8902 °2-0.0476 °2--0.9345 °2
S0.0089 Å °-0.3312 Å °0.3901 Å °0.1207 Å °0.0199 Å °-0.019 Å °-0.073 Å °-0.0161 Å °-0.0181 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 235
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB1 - 235
4X-RAY DIFFRACTION1allB301
5X-RAY DIFFRACTION1allM1 - 4
6X-RAY DIFFRACTION1allD1 - 186

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