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- PDB-1oi7: The Crystal Structure of Succinyl-CoA synthetase alpha subunit fr... -

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Basic information

Entry
Database: PDB / ID: 1oi7
TitleThe Crystal Structure of Succinyl-CoA synthetase alpha subunit from Thermus Thermophilus
ComponentsSUCCINYL-COA SYNTHETASE ALPHA CHAIN
KeywordsSYNTHETASE / SUCCINYL-COA SYNTHETASE / SCS / LIGASE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding
Similarity search - Function
Succinyl-CoA ligase, alpha subunit / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like ...Succinyl-CoA ligase, alpha subunit / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinate--CoA ligase [GDP-forming] subunit alpha
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsTakahashi, H. / Tokunaga, Y. / Kuroishi, C. / Babayeva, N. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H.
CitationJournal: To be Published
Title: The Crystal Structure of Succinyl-Coa Synthetase from Thermus Thermophilus
Authors: Takahashi, H. / Tokunaga, Y. / Kuroishi, C. / Babayeba, N. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H.
History
DepositionJun 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUCCINYL-COA SYNTHETASE ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)29,8731
Polymers29,8731
Non-polymers00
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.540, 61.540, 60.877
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SUCCINYL-COA SYNTHETASE ALPHA CHAIN / SUCCINYL-COA SYNTHETASE / SCS-ALPHA / SUCD SCSA


Mass: 29872.506 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET 11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P09143, succinate-CoA ligase (ADP-forming)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ATP + SUCCINATE + COA = ADP + SUCCINYL-COA + PHOSPHATE. PATHWAY: TRICARBOXYLIC ...CATALYTIC ACTIVITY: ATP + SUCCINATE + COA = ADP + SUCCINYL-COA + PHOSPHATE. PATHWAY: TRICARBOXYLIC ACID CYCLE. ENGINEERED MUTATION IN CHAIN A: ASP 29 TO THR 29 ENGINEERED MUTATION IN CHAIN A: THR 45 TO MET 45

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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: 2.3 Å3/Da / Density % sol: 43.5 %
Crystal growpH: 8.6
Details: PROTEIN WAS CRYSTALLIZED FROM 22.5% PEG 4000, 100 MM CHES,, pH 8.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 74888 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 34.9
Reflection shellResolution: 1.23→1.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 10.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SCU

1scu


Resolution: 1.23→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1619148.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 7418 10.1 %RANDOM
Rwork0.178 ---
obs0.178 73570 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.5 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.35 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 0 419 2391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 1.23→1.31 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 1162 9.7 %
Rwork0.209 10764 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM

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