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- PDB-2fp4: Crystal structure of pig GTP-specific succinyl-CoA synthetase in ... -

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Basic information

Entry
Database: PDB / ID: 2fp4
TitleCrystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GTP
Components(Succinyl-CoA ligase [GDP-forming] ...) x 2
KeywordsLIGASE / Active site phosphohistidine residue
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / 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
GUANOSINE-5'-TRIPHOSPHATE / : / 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: 2.08 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 15, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)75,9146
Polymers74,8052
Non-polymers1,1104
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-33 kcal/mol
Surface area26700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.610, 132.610, 72.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Succinyl-CoA ligase [GDP-forming] ... , 2 types, 2 molecules AB

#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)

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Non-polymers , 4 types, 298 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 5 mM GTP, 10 mM MgCl2, 20% w/v polylethylene glycol 3350, 150 mM KF, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 16, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.08→116.038 Å / Num. all: 43486 / Num. obs: 43486 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRsym value
2.1-2.2197.53.60.36222225462100.362
2.21-2.3599.94.80.3162.12902960180.316
2.35-2.511005.80.1953.73251456340.195
2.51-2.7110060.1375.33121452400.137
2.71-2.971006.10.0888.12951148620.088
2.97-3.321006.10.05512.52689744160.055
3.32-3.831006.10.03617.92353038850.036
3.83-4.710060.026241985132880.026
4.7-6.6410060.024251543525770.024
6.64-72.9999.75.60.01928.6806714420.019

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Phasing

Phasing MRRfactor: 0.439 / Cor.coef. Fo:Fc: 0.433 / Cor.coef. Io to Ic: 0.444
Highest resolutionLowest resolution
Rotation4 Å20 Å
Translation4 Å20 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→116.038 Å / FOM work R set: 0.834 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2235 5.1 %RANDOM
Rwork0.195 ---
all0.214 43486 --
obs0.214 43486 99.3 %-
Solvent computationBsol: 56.276 Å2
Displacement parametersBiso mean: 30.571 Å2
Baniso -1Baniso -2Baniso -3
1-1.239 Å2-1.674 Å20 Å2
2--1.239 Å20 Å2
3----2.477 Å2
Refinement stepCycle: LAST / Resolution: 2.08→116.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 66 294 5586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 44

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.08-2.10.324490.275828877
2.1-2.110.307530.264883936
2.11-2.130.299590.26906965
2.13-2.150.329430.258907950
2.15-2.170.301480.241927975
2.17-2.180.296440.241948992
2.18-2.20.239460.242908954
2.2-2.220.292380.243957995
2.22-2.240.338460.275940986
2.24-2.270.355550.253915970
2.27-2.290.296480.2249521000
2.29-2.310.338590.234936995
2.31-2.340.276420.222946988
2.34-2.360.263610.203927988
2.36-2.390.206440.19943987
2.39-2.420.316470.23945992
2.42-2.450.297510.215937988
2.45-2.480.212460.178940986
2.48-2.510.283600.1969491009
2.51-2.550.265540.217916970
2.55-2.580.252520.205944996
2.58-2.620.235460.205940986
2.62-2.660.221490.1899601009
2.66-2.710.312540.203936990
2.71-2.750.262570.196927984
2.75-2.80.288500.1999561006
2.8-2.860.23600.19900960
2.86-2.910.258550.1959571012
2.91-2.980.252410.197936977
2.98-3.050.264490.213949998
3.05-3.120.264400.2139601000
3.12-3.210.364340.208954988
3.21-3.30.2560.1929581014
3.3-3.410.242520.205928980
3.41-3.530.287540.1919551009
3.53-3.670.217490.193946995
3.67-3.840.223540.192926980
3.84-4.040.222660.1699551021
4.04-4.290.194530.164942995
4.29-4.630.206460.1529551001
4.63-5.090.185630.1519581021
5.09-5.830.293570.1959471004
5.83-7.340.205520.1789651017
7.34-2000.133530.1469871040
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_nep_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4gtp_xplor_par.txt

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