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- PDB-4g7a: The crystal structure of an alpha Carbonic Anhydrase from the ext... -

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Basic information

Entry
Database: PDB / ID: 4g7a
TitleThe crystal structure of an alpha Carbonic Anhydrase from the extremophilic bacterium Sulfurihydrogenibium yellowstonense YO3AOP1
ComponentsCarbonate dehydratase
KeywordsLYASE
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / 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, prokaryotic-like / 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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesSulfurihydrogenibium sp. YO3AOP1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDi Fiore, A. / De Simone, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: X-ray structure of the first `extremo-{alpha}-carbonic anhydrase', a dimeric enzyme from the thermophilic bacterium Sulfurihydrogenibium yellowstonense YO3AOP1.
Authors: Di Fiore, A. / Capasso, C. / De Luca, V. / Monti, S.M. / Carginale, V. / Supuran, C.T. / Scozzafava, A. / Pedone, C. / Rossi, M. / De Simone, G.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonate dehydratase
B: Carbonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0836
Polymers57,5082
Non-polymers5754
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-93 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.50, 68.36, 74.69
Angle α, β, γ (deg.)90.00, 106.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonate dehydratase / alpha-Carbonic Anhydrase


Mass: 28754.062 Da / Num. of mol.: 2 / Fragment: UNP residues 21-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurihydrogenibium sp. YO3AOP1 (bacteria)
Gene: SYO3AOP1_0578 / Production host: Escherichia coli (E. coli) / References: UniProt: B2V8E3, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% w/v PEG3350, 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 42233 / Num. obs: 42233 / % possible obs: 97.4 %
Reflection shellResolution: 1.8→1.86 Å / % possible all: 81.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 2052 4.7 %RANDOM
Rwork0.1679 39041 --
obs-41093 94.4 %-
Solvent computationBsol: 46.5303 Å2
Displacement parametersBiso max: 49.7 Å2 / Biso mean: 17.9678 Å2 / Biso min: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.899 Å20 Å2-1.747 Å2
2---1.928 Å20 Å2
3---0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 28 564 4278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.351
X-RAY DIFFRACTIONc_mcbond_it1.1481.5
X-RAY DIFFRACTIONc_scbond_it2.0442
X-RAY DIFFRACTIONc_mcangle_it1.6672
X-RAY DIFFRACTIONc_scangle_it3.0892.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3ion_anna.paramion_anna2.top
X-RAY DIFFRACTION4azm2.paramazm2.top

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