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- PDB-3o98: Glutathionylspermidine synthetase/amidase C59A complex with ADP a... -

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Basic information

Entry
Database: PDB / ID: 3o98
TitleGlutathionylspermidine synthetase/amidase C59A complex with ADP and Gsp
ComponentsBifunctional glutathionylspermidine synthetase/amidase
KeywordsLigase / Hydrolase
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 / GLUTATHIONYLSPERMIDINE / Bifunctional glutathionylspermidine synthetase/amidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPai, C.H. / Lin, C.H. / Wang, A.H.-J.
Citation
Journal: Protein Sci. / Year: 2011
Title: Structure and mechanism of Escherichia coli glutathionylspermidine amidase belonging to the family of cysteine; histidine-dependent amidohydrolases/peptidases
Authors: Pai, C.-H. / Wu, H.-J. / Lin, C.-H. / Wang, A.H.-J.
#1: Journal: 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
DepositionAug 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2011Group: Advisory / Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: Bifunctional glutathionylspermidine synthetase/amidase
B: Bifunctional glutathionylspermidine synthetase/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5469
Polymers141,1592
Non-polymers1,3867
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-16 kcal/mol
Surface area47680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.38, 76.20, 84.22
Angle α, β, γ (deg.)70.81, 74.37, 78.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bifunctional glutathionylspermidine synthetase/amidase / Glutathionylspermidine synthase / Glutathione:spermidine ligase [ADP-forming] / GSP synthetase / ...Glutathionylspermidine synthase / Glutathione:spermidine ligase [ADP-forming] / GSP synthetase / Glutathionylspermidine amidase / Glutathionylspermidine amidohydrolase [spermidine-forming] / GSP amidase


Mass: 70579.672 Da / Num. of mol.: 2 / Mutation: C59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET22b / Production host: Escherichia coli (E. coli)
References: UniProt: P0AES0, glutathionylspermidine synthase, glutathionylspermidine amidase
#2: Chemical ChemComp-TS5 / GLUTATHIONYLSPERMIDINE


Mass: 434.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H34N6O5S
#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG 3350, 0.5M MgCl2, 0.1M Tris pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 32519 / Num. obs: 31316 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.9
Reflection shellResolution: 2.8→2.9 Å / % possible all: 94.7

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2iob

2iob


Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2624 1275 random
Rwork0.2197 --
all0.2408 32919 -
obs-31316 -
Refine analyze
ObsFree
Luzzati d res low5 Å-
Luzzati sigma a0.43 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9672 0 87 206 9965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.33287
X-RAY DIFFRACTIONc_bond_d0.010238
X-RAY DIFFRACTIONc_dihedral_angle_d23.24391
X-RAY DIFFRACTIONc_improper_angle_d0.85283
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree: 0.3278 / Rfactor Rwork: 0.2808

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