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- PDB-6no0: ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA ... -

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Basic information

Entry
Database: PDB / ID: 6no0
TitleADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase
ComponentsSuccinate--CoA ligase [ADP-forming] subunit beta
KeywordsLIGASE / Complex
Function / homology
Function and homology information


hydrogenosome / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / 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: 2.209 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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
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

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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)56,1858
Polymers55,2222
Non-polymers9636
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-54 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.203, 116.981, 127.161
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:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 25 or resid 30...A1 - 25
121(chain A and (resid 1 through 25 or resid 30...A30
131(chain A and (resid 1 through 25 or resid 30...A32 - 78
141(chain A and (resid 1 through 25 or resid 30...A80 - 102
151(chain A and (resid 1 through 25 or resid 30...A0
161(chain A and (resid 1 through 25 or resid 30...A109
171(chain A and (resid 1 through 25 or resid 30...A1 - 233
181(chain A and (resid 1 through 25 or resid 30...A1 - 233
191(chain A and (resid 1 through 25 or resid 30...A154 - 156
1101(chain A and (resid 1 through 25 or resid 30...A154 - 156
1111(chain A and (resid 1 through 25 or resid 30...A169 - 232
211(chain B and (resid 1 through 25 or resid 30...B1 - 25
221(chain B and (resid 1 through 25 or resid 30...B30
231(chain B and (resid 1 through 25 or resid 30...B32 - 78
241(chain B and (resid 1 through 25 or resid 30...B80 - 102
251(chain B and (resid 1 through 25 or resid 30...B0
261(chain B and (resid 1 through 25 or resid 30...B109
271(chain B and (resid 1 through 25 or resid 30...B1 - 234
281(chain B and (resid 1 through 25 or resid 30...B1 - 234
291(chain B and (resid 1 through 25 or resid 30...B154 - 156
2101(chain B and (resid 1 through 25 or resid 30...B158 - 160
2111(chain B and (resid 1 through 25 or resid 30...B169 - 232

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Components

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


Mass: 27611.057 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253
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.: 87 / 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: 60.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 10% w/v PEG3350, 100 mM MES, pH 5.7, 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: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.209→43.05 Å / Num. obs: 34802 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.21-2.276.60.8521100
9.88-43.0560.034198.8

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 2.209→37.323 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 31.43
RfactorNum. reflection% reflection
Rfree0.2387 1625 4.68 %
Rwork0.2126 --
obs0.2138 34739 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 258.38 Å2 / Biso mean: 94.8876 Å2 / Biso min: 40.24 Å2
Refinement stepCycle: final / Resolution: 2.209→37.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 88 87 3719
Biso mean--105.7 62.75 -
Num. residues----463
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1906X-RAY DIFFRACTION3.906TORSIONAL
12B1906X-RAY DIFFRACTION3.906TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2086-2.27360.4611310.42942688281998
2.2736-2.3470.39221350.38827182853100
2.347-2.43090.34781220.344127412863100
2.4309-2.52820.32011540.301826932847100
2.5282-2.64320.28961400.25327492889100
2.6432-2.78250.25651230.229427542877100
2.7825-2.95680.22471310.222827542885100
2.9568-3.1850.25291370.228727412878100
3.185-3.50530.25551300.216227802910100
3.5053-4.0120.2191470.190327712918100
4.012-5.05270.1711320.161328132945100
5.0527-37.3280.22921430.192829123055100
Refinement TLS params.Method: refined / Origin x: -11.9643 Å / Origin y: 12.3427 Å / Origin z: 12.1848 Å
111213212223313233
T0.5366 Å20.0221 Å20.0157 Å2-0.554 Å2-0.1031 Å2--0.4901 Å2
L2.4878 °20.0029 °2-0.3694 °2-0.8526 °20.101 °2--1.0846 °2
S0.0075 Å °-0.4534 Å °0.5219 Å °0.1039 Å °0.0315 Å °-0.0678 Å °-0.1147 Å °-0.1221 Å °-0.0025 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 233
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB1 - 234
4X-RAY DIFFRACTION1allB301
5X-RAY DIFFRACTION1allM1 - 4
6X-RAY DIFFRACTION1allD1 - 87

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