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- PDB-2iob: E. coli Bifunctional glutathionylspermidine synthetase/amidase Ap... -

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Basic information

Entry
Database: PDB / ID: 2iob
TitleE. coli Bifunctional glutathionylspermidine synthetase/amidase Apo protein
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
Bifunctional glutathionylspermidine synthetase/amidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional glutathionylspermidine synthetase/amidase
B: Bifunctional glutathionylspermidine synthetase/amidase


Theoretical massNumber of molelcules
Total (without water)141,2232
Polymers141,2232
Non-polymers00
Water22,0501224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-10 kcal/mol
Surface area46870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.267, 92.964, 108.296
Angle α, β, γ (deg.)90.0, 109.373, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1224 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG 3350, 0.6M magnesium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B211
SYNCHROTRONSPring-8 BL12B220.9797, 0.9799, 0.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 11, 2004
ADSC QUANTUM 42CCDNov 11, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
30.97991
40.95371
ReflectionResolution: 2.2→50 Å / Num. obs: 70953 / Redundancy: 4.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.8

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
XTALVIEWrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.236 -random
Rwork0.1755 --
obs-67294 -
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9326 0 0 1224 10550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0197
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_deg1.929
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d24.99925
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.20322
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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