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- PDB-1cqi: Crystal Structure of the Complex of ADP and MG2+ with Dephosphory... -

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Basic information

Entry
Database: PDB / ID: 1cqi
TitleCrystal Structure of the Complex of ADP and MG2+ with Dephosphorylated E. Coli Succinyl-CoA Synthetase
Components(PROTEIN (SUCCINYL-COA SYNTHETASE ...) x 2
KeywordsLIGASE / ATP-GRASP FOLD / ROSSMANN FOLD
Function / homologyATP-grasp fold / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-citrate lyase/succinyl-CoA ligase / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / CoA-binding / Succinyl-CoA synthetase-like / ATP-citrate lyase/succinyl-CoA ligase, active site / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase/succinyl-CoA ligase, conserved site ...ATP-grasp fold / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-citrate lyase/succinyl-CoA ligase / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / CoA-binding / Succinyl-CoA synthetase-like / ATP-citrate lyase/succinyl-CoA ligase, active site / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / NAD(P)-binding domain superfamily / CoA-ligase / CoA binding domain / ATP-grasp domain / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-grasp fold profile. / ATP-grasp fold, subdomain 1 / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / succinate metabolic process / nucleoside triphosphate biosynthetic process / nucleoside diphosphate kinase activity / cofactor binding / tricarboxylic acid cycle / protein autophosphorylation / nucleotide binding / magnesium ion binding / ATP binding / cytosol / cytoplasm / 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
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3.3 Å resolution
AuthorsJoyce, M.A. / Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T.
Citation
Journal: Biochemistry / Year: 2000
Title: ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.
Authors: Joyce, M.A. / Fraser, M.E. / James, M.N. / Bridger, W.A. / Wolodko, W.T.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: A Detailed Structural Description of Escherichia Coli Succinyl-Coa Synthetase
Authors: Fraser, M.E. / James, M.N.G. / Bridger, W.A. / Wolodko, W.T.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: The Crystal Structure of Succinyl-Coa Synthetase from Escherichia Coli at 2.5A Resolution
Authors: Wolodko, W.T. / Fraser, M.E. / James, M.N.G. / Bridger, W.A.
#3: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 6, 1999 / Release: Jan 7, 2000
RevisionDateData content typeGroupCategoryProviderType
1.0Jan 7, 2000Structure modelrepositoryInitial release
1.1Oct 21, 2007Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SUCCINYL-COA SYNTHETASE ALPHA CHAIN)
B: PROTEIN (SUCCINYL-COA SYNTHETASE BETA CHAIN)
D: PROTEIN (SUCCINYL-COA SYNTHETASE ALPHA CHAIN)
E: PROTEIN (SUCCINYL-COA SYNTHETASE BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,74812
Polyers141,1204
Non-polymers2,6288
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)99.860, 99.860, 407.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP 43 2 2

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Components

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PROTEIN (SUCCINYL-COA SYNTHETASE ... , 2 types, 4 molecules ADBE

#1: Protein/peptide PROTEIN (SUCCINYL-COA SYNTHETASE ALPHA CHAIN) / E.C.6.2.1.5 / SCS-ALPHA


Mass: 29436.902 Da / Num. of mol.: 2 / Fragment: ALPHA SUBUNIT / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: UniProt: P07459, UniProt: P0AGE9*PLUS, succinate-CoA ligase (ADP-forming)
#2: Protein/peptide PROTEIN (SUCCINYL-COA SYNTHETASE BETA CHAIN) / E.C.6.2.1.5 / SCS-BETA


Mass: 41123.152 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: UniProt: P07460, UniProt: P0A836*PLUS, succinate-CoA ligase (ADP-forming)

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 767.534 Da / Num. of mol.: 2 / Formula: C21H36N7O16P3S / Coenzyme A
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 3.59 / Density percent sol: 65.78 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.3
Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, COENZYME A, pH 7.30, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temp: 21 ℃ / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
11.9 Mammonium sulfate11
20.1 Mpotassium phosphate11
31 mMdithiothreitol11
40.1 mMCoA11
50.1 mMEDTA11

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Data collection

DiffractionMean temperature: 283
SourceSource: SYNCHROTRON / Type: PHOTON FACTORY BEAMLINE BL-6A / Synchrotron site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Collection date: Jun 8, 1996
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 / Relative weight: 1
ReflectionB iso Wilson estimate: 22.8 / D resolution high: 3.3 / D resolution low: 2 / Number all: 31753 / Number obs: 31753 / Observed criterion sigma I: 0 / Rmerge I obs: 0.164 / Redundancy: 6.3 % / Percent possible obs: 99
Reflection shellRmerge I obs: 0.378 / Highest resolution: 3.3 / Lowest resolution: 3.5 / Redundancy: 3.5 % / Percent possible all: 98.4
Reflection
*PLUS
Number measured all: 195264
Reflection shell
*PLUS
Lowest resolution: 3.54 / Number unique obs: 15389

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Processing

Software
NameVersionClassification
BIOMOLPACKAGEmodel building
CNSrefinement
WEISdata reduction
SCALKB2data scaling
KBAPLYdata scaling
RefineDetails: MAXIMUM LIKELIHOOD REFINEMENT IN CNS / R Free selection details: RANDOM / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: ENGH & HUBER
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 10 / Solvent model param ksol: 0.217
Displacement parametersB iso mean: 34.7
Least-squares processR factor R free: 0.247 / R factor R free error: 0.004 / R factor R work: 0.191 / R factor obs: 0.191 / Highest resolution: 3.3 / Lowest resolution: 2 / Number reflection R free: 3470 / Number reflection obs: 31753 / Percent reflection R free: 10.9 / Percent reflection obs: 99
Refine analyzeLuzzati coordinate error free: 0.46 / Luzzati coordinate error obs: 0.34 / Luzzati d res low obs: 2 / Luzzati sigma a free: 0.51 / Luzzati sigma a obs: 0.42
Refine hist #LASTHighest resolution: 3.3 / Lowest resolution: 2
Number of atoms included #LASTProtein: 9892 / Nucleic acid: 0 / Ligand: 162 / Solvent: 0 / Total: 10054
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.0
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.10
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints ncsNcs model details: CONSTR
Refine LS shellHighest resolution: 3.3 / R factor R free: 0.338 / R factor R free error: 0.014 / R factor R work: 0.29 / Lowest resolution: 3.51 / Number reflection R free: 575 / Number reflection R work: 4543 / Total number of bins used: 6 / Percent reflection R free: 11.2 / Percent reflection obs: 98.1
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.0
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.10

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