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- PDB-6no4: ADP bound to L227bF mutant ATP-grasp fold of Blastocystis hominis... -

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Basic information

Entry
Database: PDB / ID: 6no4
TitleADP bound to L227bF 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, A domain / ATP-grasp fold, subdomain 1 ...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, A domain / ATP-grasp fold, subdomain 1 / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta
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: 2.24 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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)55,7424
Polymers55,2902
Non-polymers4522
Water1,17165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-25 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.252, 95.787, 68.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 27645.072 Da / Num. of mol.: 2 / Fragment: UNP residues 16-253 / Mutation: L227F
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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 12% w/v PEG3350, 100 mM MES, pH 6.0, 180 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: Jun 23, 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: 2.24→79.26 Å / Num. obs: 25793 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.24-2.36.60.788199.4
10.02-79.265.40.054199.9

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3311refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 2.24→68.873 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.97
RfactorNum. reflection% reflection
Rfree0.2552 1280 4.97 %
Rwork0.2138 --
obs0.2158 25761 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 233.02 Å2 / Biso mean: 86.085 Å2 / Biso min: 40.77 Å2
Refinement stepCycle: final / Resolution: 2.24→68.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 43 65 3467
Biso mean--74.41 58.97 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.32970.34341450.31342670281599
2.3297-2.43580.31881370.292656279399
2.4358-2.56420.29931420.27032682282499
2.5642-2.72490.26811400.25272669280999
2.7249-2.93530.28921470.25392684283199
2.9353-3.23060.28611520.233726932845100
3.2306-3.69810.30031360.221327372873100
3.6981-4.65910.24661390.179627782917100
4.6591-68.90520.20821420.196729123054100
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)
10.26550.14570.4320.20450.13750.4693-0.50790.89251.35620.07360.4201-0.4127-1.1014-1.0178-0.011.0433-0.0220.01071.2070.1991.130130.632444.60532.6189
21.1068-0.5608-0.62673.1066-0.3711.93120.24820.11370.37450.0581-0.09550.4824-0.0654-0.563800.5265-0.02770.02220.6173-0.05980.596919.219337.3646-14.3149
32.15621.0919-1.062.2762-0.10613.92720.1119-0.47720.07090.2791-0.14480.1616-0.32480.2828-0.00010.5851-0.1142-0.02030.64140.01410.491324.486631.733310.5498
40.94530.73380.49733.3747-2.57774.07880.85540.6734-0.24050.77090.03290.0203-2.41230.14970.94880.95050.23920.18430.6612-0.14340.622142.248933.7286-28.9241
51.5158-0.1986-0.77341.6222-0.4371.56580.3052-0.16720.29350.2428-0.2086-0.1428-0.0830.194100.5085-0.0203-0.01990.4718-0.03580.532948.095237.0093-10.5444
61.2212-1.3739-1.6616-0.850.22614.80980.00110.6807-0.50140.0823-0.30110.13770.1782-0.3458-0.02530.5930.00820.02110.6581-0.21190.64944.694819.3971-32.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:19)A1 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:114)A20 - 114
3X-RAY DIFFRACTION3(chain A and resid 115:233)A115 - 233
4X-RAY DIFFRACTION4(chain B and resid 3:20)B3 - 20
5X-RAY DIFFRACTION5(chain B and resid 21:113)B21 - 113
6X-RAY DIFFRACTION6(chain B and resid 114:233)B114 - 233

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