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- PDB-3a2z: E. coli Gsp amidase Cys59 sulfenic acid -

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Basic information

Entry
Database: PDB / ID: 3a2z
TitleE. coli Gsp amidase Cys59 sulfenic acid
ComponentsBifunctional glutathionylspermidine synthetase/amidase
KeywordsHydrolase / Ligase / Gsp amidase / ATP-binding / Multifunctional enzyme / Nucleotide-binding
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPai, C.-H. / Ko, T.-P. / Chiang, B.-Y. / Lin, C.-H. / Wang, A.H.-J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Protein S-thiolation by Glutathionylspermidine (Gsp): the role of Escherichia coli Gsp synthetASE/amidase in redox regulation
Authors: Chiang, B.-Y. / Chen, T.-C. / Pai, C.-H. / Chou, C.-C. / Chen, H.-H. / Ko, T.-P. / Hsu, W.-H. / Chang, C.-Y. / Wu, W.-F. / Wang, A.H.-J. / Lin, C.-H.
History
DepositionJun 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 10, 2021Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)22,2941
Polymers22,2941
Non-polymers00
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bifunctional glutathionylspermidine synthetase/amidase

A: Bifunctional glutathionylspermidine synthetase/amidase


Theoretical massNumber of molelcules
Total (without water)44,5882
Polymers44,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2710 Å2
ΔGint-6 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.902, 83.902, 106.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-534-

HOH

31A-670-

HOH

41A-792-

HOH

51A-814-

HOH

61A-855-

HOH

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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: 22293.912 Da / Num. of mol.: 1 / Fragment: residues 1-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: gsp, b2988, JW2956 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AES0, glutathionylspermidine synthase, glutathionylspermidine amidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACCORDING TO THE DEPOSITOR, THEY OBSERVED THE MODIFICATION ON CYS59 WITH EXTENDED DENSITY MAP, AND ...ACCORDING TO THE DEPOSITOR, THEY OBSERVED THE MODIFICATION ON CYS59 WITH EXTENDED DENSITY MAP, AND INTERPRET THIS CYS59 AS CYS-S-O, THE SULFENIC ACID IN THIS ENTRY. HYDROGEN PEROXIDE CONSIST OF HOH A 900 AND 901 DONATED OXYGEN OF CYS-S-O. SINCE IT WAS KIND OF LIKE AN INTERMEDIATE, THE DISTANCE OF S-O IS LARGER THAN IT USUALLY IS.

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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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 4.5
Details: 0.1M acetate, 0.8M NaH2PO4, 1.2M K2HPO4, pH 4.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 35956 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 17 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 77.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 15.1 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3519

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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: 1.5→25 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1719 4.8 %random
Rwork0.1801 32932 --
all-36041 --
obs-34651 96.1 %-
Solvent computationBsol: 48.923 Å2
Displacement parametersBiso max: 60.21 Å2 / Biso mean: 26.201 Å2 / Biso min: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.079 Å2-0.92 Å20 Å2
2---1.079 Å20 Å2
3---2.158 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 0 364 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4931.5
X-RAY DIFFRACTIONc_scbond_it2.2332
X-RAY DIFFRACTIONc_mcangle_it2.3972
X-RAY DIFFRACTIONc_scangle_it3.282.5
X-RAY DIFFRACTIONc_angle_deg1.8658
X-RAY DIFFRACTIONc_bond_d0.0201
LS refinement shellResolution: 1.5→1.55 Å
RfactorNum. reflection
Rfree0.2742 164
Rwork0.2239 -
obs-3101
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3prosth.par

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