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- PDB-2io8: E. coli Bifunctional glutathionylspermidine synthetase/amidase In... -

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Basic information

Entry
Database: PDB / ID: 2io8
TitleE. coli Bifunctional glutathionylspermidine synthetase/amidase Incomplex with Mg2+ and ADP
ComponentsBifunctional glutathionylspermidine synthetase/amidase
KeywordsLIGASE / HYDROLASE / Bifunctional glutathionylspermidine synthetase/amidase
Function / homology
Function and homology information


glutathionylspermidine amidase / glutathionylspermidine synthase / glutathionylspermidine amidase activity / glutathionylspermidine synthase activity / spermidine metabolic process / glutathione metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Glutathionylspermidine synthase, pre-ATP-grasp-like domain / : / Glutathionylspermidine synthase preATP-grasp / CHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Pre-ATP-grasp domain superfamily / Papain-like cysteine peptidase superfamily ...Glutathionylspermidine synthase, pre-ATP-grasp-like domain / : / Glutathionylspermidine synthase preATP-grasp / CHAP domain profile. / CHAP domain / CHAP domain / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Pre-ATP-grasp domain superfamily / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CYSTEINE / Bifunctional glutathionylspermidine synthetase/amidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPai, C.H. / Chiang, B.Y. / Ko, T.P. / Chou, C.C. / Chong, C.M. / Yen, F.J. / Coward, J.K. / Wang, A.H.-J. / Lin, C.H.
CitationJournal: Embo J. / Year: 2006
Title: Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase
Authors: Pai, C.H. / Chiang, B.Y. / Ko, T.P. / Chou, C.C. / Chong, C.M. / Yen, F.J. / Chen, S. / Coward, J.K. / Wang, A.H.-J. / Lin, C.H.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_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: Bifunctional glutathionylspermidine synthetase/amidase
B: Bifunctional glutathionylspermidine synthetase/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,41710
Polymers141,2232
Non-polymers1,1948
Water16,033890
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-76 kcal/mol
Surface area46040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.20, 75.61, 84.44
Angle α, β, γ (deg.)70.17, 73.92, 77.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bifunctional glutathionylspermidine synthetase/amidase / Glutathionylspermidine synthase / Glutathionylspermidine amidase


Mass: 70611.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET22b (Novagen) / Production host: Escherichia coli (E. coli)
References: UniProt: P0AES0, glutathionylspermidine synthase, glutathionylspermidine amidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 12% PEG 3350, 0.5M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 75954 / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.8
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2947

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
XTALVIEWrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflectionSelection details
Rfree0.2363 -random
Rwork0.1735 --
obs-63960 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9574 0 80 882 10536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0117
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.613
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d24.63232
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d0.96136
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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