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- PDB-2yv2: Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Aer... -

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Basic information

Entry
Database: PDB / ID: 2yv2
TitleCrystal Structure of Succinyl-CoA Synthetase Alpha Chain from Aeropyrum pernix K1
ComponentsSuccinyl-CoA synthetase alpha chain
KeywordsLIGASE / CoA-binding domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) activity / succinate-CoA ligase (ADP-forming) / 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 [ADP-forming] subunit alpha
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNiwa, H. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Succinyl-CoA Synthetase Alpha Chain from Aeropyrum pernix K1
Authors: Niwa, H. / Kuramitsu, S. / Yokoyama, S.
History
DepositionApr 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)31,5081
Polymers31,5081
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.542, 137.183, 74.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Succinyl-CoA synthetase alpha chain


Mass: 31508.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: sucD / Plasmid: pET-21a / Production host: Escherichia coli (E. coli)
References: UniProt: Q9YD40, succinate-CoA ligase (ADP-forming)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8
Details: 50% Ethylene glycol, 0.1M imidazole, pH8.0, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 11, 2006
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 15880 / Num. obs: 15880 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 7 / Num. unique all: 1549 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OI7

1oi7


Resolution: 2.2→44.13 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2051748.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1215 7.7 %RANDOM
Rwork0.201 ---
obs0.201 15864 99.7 %-
all-15864 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5403 Å2 / ksol: 0.354709 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.7 Å20 Å20 Å2
2--6.99 Å20 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 0 184 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 199 7.8 %
Rwork0.203 2349 -
obs-2548 97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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