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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 / 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 / cytoplasm / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / COENZYME A / PHOSPHATE ION / 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 / Resolution: 3.3 Å
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.
History
DepositionAug 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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 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
Polymers141,1204
Non-polymers2,6288
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP4322

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Components

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

#1: Protein 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 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 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 6

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % 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
Temperature: 21 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common 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 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 8, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 31753 / Num. obs: 31753 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.164
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.378 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 195264
Reflection shell
*PLUS
Lowest resolution: 3.54 Å / Num. unique obs: 15389

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Processing

Software
NameVersionClassification
BIOMOLPACKAGEmodel building
CNSrefinement
WEISdata reduction
SCALKB2data scaling
KBAPLYdata scaling
RefinementResolution: 3.3→20 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD REFINEMENT IN CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3470 10.9 %RANDOM
Rwork0.191 ---
obs0.191 31753 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.217 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-20 Å
Luzzati sigma a0.51 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9892 0 162 0 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
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
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
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 575 11.2 %
Rwork0.29 4543 -
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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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