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- PDB-2fpi: Crystal structure of pig GTP-specific succinyl-CoA synthetase fro... -

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Basic information

Entry
Database: PDB / ID: 2fpi
TitleCrystal structure of pig GTP-specific succinyl-CoA synthetase from polyethylene glycol
Components
  • Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial
  • Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial
KeywordsLIGASE / Active site Phosphohistidine residue
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / GTP binding / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / 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. ...Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / 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. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Isoform I of Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFraser, M.E.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Interactions of GTP with the ATP-grasp Domain of GTP-specific Succinyl-CoA Synthetase
Authors: Fraser, M.E. / Hayakawa, K. / Hume, M.S. / Ryan, D.G. / Brownie, E.R.
History
DepositionJan 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial
B: Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9974
Polymers74,8052
Non-polymers1922
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-55 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.790, 135.790, 77.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial / Succinyl-CoA synthetase / alpha chain / SCS-alpha


Mass: 32168.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O19069-2, UniProt: O19069*PLUS, succinate-CoA ligase (GDP-forming)
#2: Protein Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial / Succinyl-CoA synthetase / betaG chain / SCS-betaG / GTP- specific succinyl-CoA synthetase beta ...Succinyl-CoA synthetase / betaG chain / SCS-betaG / GTP- specific succinyl-CoA synthetase beta subunit / Fragment


Mass: 42635.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG2 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53590, succinate-CoA ligase (GDP-forming)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: P4K, isopropanol, ammonium sulfate and bicine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2001
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 14.3 / Number: 134763 / Rmerge(I) obs: 0.049 / Χ2: 0.96 / D res high: 2.7 Å / D res low: 100 Å / Num. obs: 22742 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squared
7.33100115896.710.0331.082
5.827.33115710010.0320.896
5.085.82114210010.0340.912
4.625.08114410010.0330.956
4.294.62113510010.0340.995
4.034.29115410010.0360.925
3.834.03112799.910.0411.026
3.663.83114310010.0571.31
3.523.66114399.810.0511.031
3.43.52111210010.0550.985
3.33.4115110010.0660.966
3.23.3112410010.0810.946
3.123.2113510010.0980.951
3.043.12113410010.1080.931
2.973.04112599.910.1380.918
2.912.97110610010.1590.917
2.852.91114810010.1880.885
2.82.85113410010.2130.884
2.752.8113310010.2390.868
2.72.75113710010.2580.848
ReflectionResolution: 2.7→100 Å / Num. all: 22742 / Num. obs: 22742 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Χ2: 0.963 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.75 Å / % possible obs: 100 % / Rmerge(I) obs: 0.258 / Num. unique obs: 1137 / Χ2: 0.848 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→100 Å / FOM work R set: 0.737 / Isotropic thermal model: ISOTROPIC / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1123 5 %RANDOM
Rwork0.215 ---
all0.22 22397 --
obs0.22 22397 99.8 %-
Solvent computationBsol: 28.166 Å2
Displacement parametersBiso mean: 45.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.122 Å2-10.896 Å20 Å2
2---0.122 Å20 Å2
3---0.244 Å2
Refinement stepCycle: LAST / Resolution: 2.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5225 0 10 64 5299
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.740.481710.3459771048
2.74-2.790.368670.294924991
2.79-2.840.322760.2489451021
2.84-2.890.393590.2689441003
2.89-2.940.393610.2979611022
2.94-30.355510.282946997
3-3.070.424610.2779591020
3.07-3.140.376440.2879661010
3.14-3.220.399330.2949731006
3.22-3.30.366490.2669701019
3.3-3.40.319310.20610071038
3.4-3.510.368450.251943988
3.51-3.640.365520.2319631015
3.64-3.780.261510.1979691020
3.78-3.950.312490.2289651014
3.95-4.160.311430.1999721015
4.16-4.420.313440.1769831027
4.42-4.770.273410.1739881029
4.77-5.250.216450.1739801025
5.25-60.329480.2039841032
6-7.570.279560.1829711027
7.57-2000.171460.1559841030
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_nep_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3ion.param

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