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- PDB-1flj: CRYSTAL STRUCTURE OF S-GLUTATHIOLATED CARBONIC ANHYDRASE III -

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Basic information

Entry
Database: PDB / ID: 1flj
TitleCRYSTAL STRUCTURE OF S-GLUTATHIOLATED CARBONIC ANHYDRASE III
ComponentsCARBONIC ANHYDRASE IIICarbonic anhydrase
KeywordsLYASE / Carbonic Anhydrase III / Glutathione / S-Glutathiolated / S-Glutathionylated
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / hydro-lyase activity / phosphatase activity / nickel cation binding / response to bacterium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / response to ethanol / response to oxidative stress ...Reversible hydration of carbon dioxide / hydro-lyase activity / phosphatase activity / nickel cation binding / response to bacterium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / response to ethanol / response to oxidative stress / zinc ion binding / cytosol
Similarity search - Function
Carbonic anhydrase, CA3 / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. ...Carbonic anhydrase, CA3 / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Carbonic anhydrase 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsMallis, R.J. / Poland, B.W. / Chatterjee, T.K. / Fisher, R.A. / Darmawan, S. / Honzatko, R.B. / Thomas, J.A.
Citation
Journal: FEBS Lett. / Year: 2000
Title: Crystal structure of S-glutathiolated carbonic anhydrase III.
Authors: Mallis, R.J. / Poland, B.W. / Chatterjee, T.K. / Fisher, R.A. / Darmawan, S. / Honzatko, R.B. / Thomas, J.A.
#1: Journal: Arch.Biochem.Biophys. / Year: 1995
Title: Protein Sulfhydryls and Their Role in the Antioxidant Function of Protein S-thiolation
Authors: Thomas, J.A. / Poland, B. / Honzatko, R.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0494
Polymers29,3691
Non-polymers6803
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.25, 44.73, 66.91
Angle α, β, γ (deg.)90., 99.73, 90.
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein CARBONIC ANHYDRASE III / Carbonic anhydrase / E.C.4.2.1.1 / CARBONATE DEHYDRATASE III / CA-III


Mass: 29369.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P14141, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, propanol, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 %(v/v)propanol1drop
315-20 %(w/v)PEG33501drop
4100 mMHEPES1drop
510 %(v/v)propanol1reservoir
615-20 %(w/v)PEG33501reservoir
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→5 Å / Num. all: 20193 / Num. obs: 20193 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.216 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.014 / Net I/σ(I): 5.4
Reflection
*PLUS
Lowest resolution: 5 Å / % possible obs: 90 % / Num. measured all: 44741 / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 1.8→5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2019 10 %random
Rwork0.155 ---
all0.155 20193 --
obs0.155 20193 71.44 %-
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 41 216 2333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.51
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 14426 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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