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- PDB-2scu: A detailed description of the structure of Succinyl-COA synthetas... -

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Basic information

Entry
Database: PDB / ID: 2scu
TitleA detailed description of the structure of Succinyl-COA synthetase from Escherichia coli
Components(PROTEIN (SUCCINYL-COA LIGASE)) x 2
KeywordsLIGASE / CITRIC ACID CYCLE / HETEROTETRAMER
Function / homology
Function and homology information


succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / ATP binding ...succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / 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, B domain / ATP-grasp fold, subdomain 1 / 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 / Succinate--CoA ligase [ADP-forming] subunit alpha / Succinate--CoA ligase [ADP-forming] subunit beta / 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 / MIR / Resolution: 2.3 Å
AuthorsFraser, M.E. / Wolodko, W.T. / James, M.N.G. / Bridger, W.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: A detailed structural description of Escherichia coli succinyl-CoA synthetase.
Authors: Fraser, M.E. / James, M.N. / Bridger, W.A. / Wolodko, W.T.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: The Crystal Structure of Succinyl-Coa Synthetase from Escherichia Coli at 2.5 Angstroms Resolution
Authors: Wolodko, W.T. / Fraser, M.E. / James, M.N.G. / Bridger, W.A.
#2: Journal: J.Biol.Chem. / Year: 1984
Title: Crystallization of Succinyl-Coa Synthetase from Escherichia Coli
Authors: Wolodko, W.T. / James, M.N.G. / Bridger, W.A.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: A Dimeric Form of Escherichia Coli Succinyl-Coa Synthetase Produced by Site- Directed Mutagenesis
Authors: Bailey, D.L. / Fraser, M.E. / Bridger, W.A. / James, M.N.G. / Wolodko, W.T.
History
DepositionSep 24, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SUCCINYL-COA LIGASE)
B: PROTEIN (SUCCINYL-COA LIGASE)
D: PROTEIN (SUCCINYL-COA LIGASE)
E: PROTEIN (SUCCINYL-COA LIGASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1218
Polymers142,3934
Non-polymers1,7274
Water9,044502
1
A: PROTEIN (SUCCINYL-COA LIGASE)
B: PROTEIN (SUCCINYL-COA LIGASE)
hetero molecules

A: PROTEIN (SUCCINYL-COA LIGASE)
B: PROTEIN (SUCCINYL-COA LIGASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1218
Polymers142,3934
Non-polymers1,7274
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area9390 Å2
ΔGint-69 kcal/mol
Surface area49910 Å2
MethodPISA
2
D: PROTEIN (SUCCINYL-COA LIGASE)
E: PROTEIN (SUCCINYL-COA LIGASE)
hetero molecules

D: PROTEIN (SUCCINYL-COA LIGASE)
E: PROTEIN (SUCCINYL-COA LIGASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1218
Polymers142,3934
Non-polymers1,7274
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area9530 Å2
ΔGint-65 kcal/mol
Surface area50000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.680, 98.680, 403.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-1166-

HOH

21D-1288-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.756672, -0.256354, -0.601439), (-0.242056, -0.744706, 0.62195), (-0.607335, 0.616195, 0.501446)90.278, 28.081, 25.009
2given(-0.756672, -0.256354, -0.601439), (-0.242056, -0.744706, 0.62195), (-0.607335, 0.616195, 0.501446)90.278, 28.081, 25.009
3given(-0.754283, -0.251541, -0.606452), (-0.247007, -0.74711, 0.617101), (-0.608313, 0.615267, 0.5014)90.591, 28.486, 25.027
4given(-0.754283, -0.251541, -0.606452), (-0.247007, -0.74711, 0.617101), (-0.608313, 0.615267, 0.5014)90.591, 28.486, 25.027

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Components

#1: Protein PROTEIN (SUCCINYL-COA LIGASE) / SCS


Mass: 29758.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES A246 AND D246 ARE PHOSPHOHISTIDINES / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CR63 / Production host: Escherichia coli (E. coli)
References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming)
#2: Protein PROTEIN (SUCCINYL-COA LIGASE) / SCS


Mass: 41438.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES A246 AND D246 ARE PHOSPHOHISTIDINES / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CR63 / Production host: Escherichia coli (E. coli)
References: UniProt: P07460, UniProt: P0A836*PLUS, succinate-CoA ligase (ADP-forming)
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSO4 400 IS ASSOCIATED WITH BETA SUBUNIT CHAIN B. SO4 401 IS ASSOCIATED WITH BETA SUBUNIT CHAIN E.
Sequence detailsAMINO-TERMINAL ANALYSIS OF THE ALPHA SUBUNIT INDICATES THAT THE FIRST RESIDUE IS A SERINE (W. A. ...AMINO-TERMINAL ANALYSIS OF THE ALPHA SUBUNIT INDICATES THAT THE FIRST RESIDUE IS A SERINE (W. A. BRIDGE, ENZYMES, 1974, 3RD ED. 10, 581-606). IN THE GENE SEQUENCING PAPER, BUCK, SPENCER AND GUEST STATE THAT [THE ASSUMPTION IS] THAT THE INITIATING FORMYLMETHIONINE IS REMOVED POSTTRANSLATIONALLY FROM THE ALPHA BUT NOT FROM THE BETA SUBUNIT (D. BUCK, M. E. SPENCER, AND J. R. GUEST, BIOCHEMISTRY 24, 6245-6252 (1985)).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 23

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.35 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD.
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.3 / Method: microdialysis / Details: Wolodko, W.T., (1984) J. Biol. Chem., 259, 5316.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme11
21.9 Mammonium sulfate12
30.1 Mpotassium phosphate12
41 mMdithiothreitol12
50.1 mMCoA12
60.1 mMEDTA12

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Mar 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 417950 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 2.3→2.5 Å / Rmerge(I) obs: 0.45
Reflection
*PLUS
Num. obs: 83411 / Num. measured all: 417950

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Processing

Software
NameVersionClassification
TNT5EBrefinement
WEISdata reduction
BIOMOL(KBRANIdata scaling
KBAPLY)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.195 --
all0.195 83411 -
obs-83411 93 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9900 0 106 502 10508
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02101601
X-RAY DIFFRACTIONt_angle_deg2.042137101
X-RAY DIFFRACTIONt_dihedral_angle_d19.19362060
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0132422
X-RAY DIFFRACTIONt_gen_planes0.02314803
X-RAY DIFFRACTIONt_it2.854101600.3
X-RAY DIFFRACTIONt_nbd0.03631310
Software
*PLUS
Name: TNT / Version: 5EB / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0132
X-RAY DIFFRACTIONt_plane_restr0.0233

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