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- PDB-1jll: Crystal Structure Analysis of the E197betaA Mutant of E. coli SCS -

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Basic information

Entry
Database: PDB / ID: 1jll
TitleCrystal Structure Analysis of the E197betaA Mutant of E. coli SCS
Components(succinyl-CoA synthetase ...) x 2
KeywordsLIGASE / CITRIC ACID CYCLE / HETEROTETRAMER / ATP-GRASP FOLD / ROSSMANN FOLD
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
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 ...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, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / 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
COENZYME A / PHOSPHATE ION / Succinate--CoA ligase [ADP-forming] subunit alpha / Succinate--CoA ligase [ADP-forming] subunit beta / Succinate--CoA ligase [ADP-forming] subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.69 Å
AuthorsFraser, M.E.
CitationJournal: Biochemistry / Year: 2002
Title: Two glutamate residues, Glu 208 alpha and Glu 197 beta, are crucial for phosphorylation and dephosphorylation of the active-site histidine residue in succinyl-CoA synthetase.
Authors: Fraser, M.E. / Joyce, M.A. / Ryan, D.G. / Wolodko, W.T.
History
DepositionJul 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: succinyl-CoA synthetase alpha subunit
B: succinyl-CoA synthetase beta subunit
D: succinyl-CoA synthetase alpha subunit
E: succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,76414
Polymers142,1194
Non-polymers3,64410
Water3,477193
1
A: succinyl-CoA synthetase alpha subunit
B: succinyl-CoA synthetase beta subunit
hetero molecules

A: succinyl-CoA synthetase alpha subunit
B: succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,76414
Polymers142,1194
Non-polymers3,64410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
2
D: succinyl-CoA synthetase alpha subunit
E: succinyl-CoA synthetase beta subunit
hetero molecules

D: succinyl-CoA synthetase alpha subunit
E: succinyl-CoA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,76414
Polymers142,1194
Non-polymers3,64410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Unit cell
Length a, b, c (Å)97.06, 97.06, 389.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Succinyl-CoA synthetase ... , 2 types, 4 molecules ADBE

#1: Protein succinyl-CoA synthetase alpha subunit / SCS-ALPHA


Mass: 29679.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming)
#2: Protein succinyl-CoA synthetase beta subunit / SCS-BETA


Mass: 41380.461 Da / Num. of mol.: 2 / Mutation: E197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A836, succinate-CoA ligase (ADP-forming)

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Non-polymers , 4 types, 203 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Bicine, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMBicine1reservoirpH7.6
21.80-2.04 Mammonium sulfate1reservoir
313.8 mg/mlprotein1drop
40.5 mMCoA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2000
Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 48720 / Num. obs: 48720 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.6 / % possible all: 61.7
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 152728
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 61.7 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1JKJ, partially refined

1jkj


Resolution: 2.69→34.38 Å
Cross valid method: THROUGHOUT. STARTED WITH 10% OF THE DATA, REDUCED THIS TO JUST OVER 1000 REFLECTIONS NEAR THE END OF THE REFINEMENT.
σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1000 -random. BUT THE REFLECTIONS CHOSEN ARE CONSISTENT AMONG ALL DATA SETS FOR THIS CRYSTAL FORM.
Rwork0.222 ---
all0.223 48023 --
obs0.223 48023 90.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 43.6307 Å2 / ksol: 0.380601 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.69→34.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9923 0 139 193 10255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.19
X-RAY DIFFRACTIONc_mcbond_it1.28
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.339 / Rfactor Rwork: 0.34 / Total num. of bins used: 4

Resolution (Å)Highest resolution (Å)Num. reflection RfreeRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.7-2.821530.027500078.2
2.8288.3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 47023 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor Rfree: 0.339 / Rfactor Rwork: 0.34

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