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- PDB-6no5: ADP bound to K46bE&K114bD mutant ATP-grasp fold of Blastocystis h... -

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Basic information

Entry
Database: PDB / ID: 6no5
TitleADP bound to K46bE&K114bD mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase
ComponentsSuccinate--CoA ligase [ADP-forming] subunit beta
KeywordsLIGASE / Double mutation / Complex
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 / AMMONIUM ION / Succinate--CoA ligase [ADP-forming] subunit beta
Similarity search - Component
Biological speciesBlastocystis sp. subtype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.069 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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
C: Succinate--CoA ligase [ADP-forming] subunit beta
D: Succinate--CoA ligase [ADP-forming] subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,26616
Polymers110,3884
Non-polymers1,87812
Water7,296405
1
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)56,1338
Polymers55,1942
Non-polymers9396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-39 kcal/mol
Surface area21800 Å2
MethodPISA
2
C: Succinate--CoA ligase [ADP-forming] subunit beta
D: Succinate--CoA ligase [ADP-forming] subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1338
Polymers55,1942
Non-polymers9396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-38 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.052, 82.494, 91.248
Angle α, β, γ (deg.)90.000, 118.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 5 or resid 8...
21(chain B and (resid 2 through 5 or resid 8...
31(chain C and (resid 2 through 5 or resid 8...
41(chain D and (resid 2 through 5 or resid 8...

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
11ASNASNGLUGLU(chain A and (resid 2 through 5 or resid 8...AA2 - 52 - 5
12SERSERGLUGLU(chain A and (resid 2 through 5 or resid 8...AA8 - 238 - 23
13ALAALALYSLYS(chain A and (resid 2 through 5 or resid 8...AA25 - 3625 - 36
14LEULEUTRPTRP(chain A and (resid 2 through 5 or resid 8...AA38 - 6338 - 63
15TRPTRPTRPTRP(chain A and (resid 2 through 5 or resid 8...AA66
16ILEILEALAALA(chain A and (resid 2 through 5 or resid 8...AA88 - 9988 - 99
17METMETPHEPHE(chain A and (resid 2 through 5 or resid 8...AA1 - 2391 - 239
18METMETPHEPHE(chain A and (resid 2 through 5 or resid 8...AA1 - 2391 - 239
19METMETPHEPHE(chain A and (resid 2 through 5 or resid 8...AA1 - 2391 - 239
110METMETPHEPHE(chain A and (resid 2 through 5 or resid 8...AA1 - 2391 - 239
111GLYGLYALAALA(chain A and (resid 2 through 5 or resid 8...AA130 - 136130 - 136
112PHEPHEILEILE(chain A and (resid 2 through 5 or resid 8...AA156 - 209156 - 209
113PROPROPHEPHE(chain A and (resid 2 through 5 or resid 8...AA211 - 233211 - 233
21ASNASNGLUGLU(chain B and (resid 2 through 5 or resid 8...BB2 - 52 - 5
22SERSERGLUGLU(chain B and (resid 2 through 5 or resid 8...BB8 - 238 - 23
23ALAALALYSLYS(chain B and (resid 2 through 5 or resid 8...BB25 - 3625 - 36
24METMETASPASP(chain B and (resid 2 through 5 or resid 8...BB1 - 2341 - 234
25GLYGLYVALVAL(chain B and (resid 2 through 5 or resid 8...BB101 - 107101 - 107
26METMETASPASP(chain B and (resid 2 through 5 or resid 8...BB1 - 2341 - 234
27VALVALVALVAL(chain B and (resid 2 through 5 or resid 8...BB109109
28GLYGLYLEULEU(chain B and (resid 2 through 5 or resid 8...BB111 - 121111 - 121
29GLYGLYALAALA(chain B and (resid 2 through 5 or resid 8...BB130 - 136130 - 136
210PHEPHEILEILE(chain B and (resid 2 through 5 or resid 8...BB156 - 209156 - 209
211PROPROPHEPHE(chain B and (resid 2 through 5 or resid 8...BB211 - 233211 - 233
31ASNASNGLUGLU(chain C and (resid 2 through 5 or resid 8...CC2 - 52 - 5
32SERSERGLUGLU(chain C and (resid 2 through 5 or resid 8...CC8 - 238 - 23
33ALAALALYSLYS(chain C and (resid 2 through 5 or resid 8...CC25 - 3625 - 36
34LEULEUTRPTRP(chain C and (resid 2 through 5 or resid 8...CC38 - 6338 - 63
35TRPTRPTRPTRP(chain C and (resid 2 through 5 or resid 8...CC66
36ILEILEALAALA(chain C and (resid 2 through 5 or resid 8...CC88 - 9988 - 99
37ASNASNPHEPHE(chain C and (resid 2 through 5 or resid 8...CC2 - 2332 - 233
38ASNASNPHEPHE(chain C and (resid 2 through 5 or resid 8...CC2 - 2332 - 233
39ASNASNPHEPHE(chain C and (resid 2 through 5 or resid 8...CC2 - 2332 - 233
310ASNASNPHEPHE(chain C and (resid 2 through 5 or resid 8...CC2 - 2332 - 233
311GLYGLYALAALA(chain C and (resid 2 through 5 or resid 8...CC130 - 136130 - 136
312PHEPHEILEILE(chain C and (resid 2 through 5 or resid 8...CC156 - 209156 - 209
313PROPROPHEPHE(chain C and (resid 2 through 5 or resid 8...CC211 - 233211 - 233
41ASNASNGLUGLU(chain D and (resid 2 through 5 or resid 8...DD2 - 52 - 5
42SERSERGLUGLU(chain D and (resid 2 through 5 or resid 8...DD8 - 238 - 23
43ALAALALYSLYS(chain D and (resid 2 through 5 or resid 8...DD25 - 3625 - 36
44TRPTRPTRPTRP(chain D and (resid 2 through 5 or resid 8...DD66
45ILEILEALAALA(chain D and (resid 2 through 5 or resid 8...DD88 - 9988 - 99
46METMETASPASP(chain D and (resid 2 through 5 or resid 8...DD1 - 2341 - 234
47VALVALVALVAL(chain D and (resid 2 through 5 or resid 8...DD109109
48GLYGLYLEULEU(chain D and (resid 2 through 5 or resid 8...DD111 - 121111 - 121
49METMETASPASP(chain D and (resid 2 through 5 or resid 8...DD1 - 2341 - 234
410GLYGLYALAALA(chain D and (resid 2 through 5 or resid 8...DD130 - 136130 - 136
411PHEPHEILEILE(chain D and (resid 2 through 5 or resid 8...DD156 - 209156 - 209
412PROPROPHEPHE(chain D and (resid 2 through 5 or resid 8...DD211 - 233211 - 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.: 4 / 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: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 15% w/v PEG3350, 100 mM MES, pH 6.6, 140 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: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.069→45.61 Å / Num. obs: 70552 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.07-2.123.20.575199.8
9.26-45.613.20.14199

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3311refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 2.069→36.648 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 25.16
RfactorNum. reflection% reflection
Rfree0.2216 3505 4.97 %
Rwork0.1943 --
obs0.1957 70490 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.27 Å2 / Biso mean: 54.1789 Å2 / Biso min: 26.33 Å2
Refinement stepCycle: final / Resolution: 2.069→36.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7088 0 192 405 7685
Biso mean--46.74 45.33 -
Num. residues----927
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3665X-RAY DIFFRACTION5.073TORSIONAL
12B3665X-RAY DIFFRACTION5.073TORSIONAL
13C3665X-RAY DIFFRACTION5.073TORSIONAL
14D3665X-RAY DIFFRACTION5.073TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0693-2.09770.29071180.28752613273199
2.0977-2.12760.32331420.289127192861100
2.1276-2.15940.29531210.290226572778100
2.1594-2.19310.31841200.280726652785100
2.1931-2.22910.3111300.307927302860100
2.2291-2.26750.3111840.280925662750100
2.2675-2.30870.35091560.288826492805100
2.3087-2.35310.28251440.248426992843100
2.3531-2.40110.30151300.236826672797100
2.4011-2.45330.25061190.22426872806100
2.4533-2.51040.24851320.217826852817100
2.5104-2.57320.26641450.215826642809100
2.5732-2.64270.26711590.215426542813100
2.6427-2.72050.27781440.215226822826100
2.7205-2.80820.22561080.206427022810100
2.8082-2.90860.23231490.204626752824100
2.9086-3.0250.21331820.212126362818100
3.025-3.16260.23141490.207426942843100
3.1626-3.32920.27221530.208726582811100
3.3292-3.53760.20671410.191526802821100
3.5376-3.81050.21581270.174727122839100
3.8105-4.19350.19511220.154627182840100
4.1935-4.79920.17051440.138426882832100
4.7992-6.0420.16841520.152127102862100
6.042-36.6540.15641340.17452775290999

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