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- PDB-4x5s: The crystal structure of an alpha carbonic anhydrase from the ext... -

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Basic information

Entry
Database: PDB / ID: 4x5s
TitleThe crystal structure of an alpha carbonic anhydrase from the extremophilic bacterium Sulfurihydrogenibium azorense.
ComponentsCarbonic anhydrase (Carbonate dehydratase)
KeywordsLYASE / Alpha bacterial carbonic anhydrase / Enzyme-inhibitor complex
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 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Carbonic anhydrase
Similarity search - Component
Biological speciesSulfurihydrogenibium azorense (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDe Simone, G. / Alterio, V. / Di Fiore, A.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Crystal structure of the most catalytically effective carbonic anhydrase enzyme known, SazCA from the thermophilic bacterium Sulfurihydrogenibium azorense.
Authors: De Simone, G. / Monti, S.M. / Alterio, V. / Buonanno, M. / De Luca, V. / Rossi, M. / Carginale, V. / Supuran, C.T. / Capasso, C. / Di Fiore, A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase (Carbonate dehydratase)
B: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6078
Polymers53,2902
Non-polymers1,3166
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-80 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.470, 89.430, 114.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase (Carbonate dehydratase)


Mass: 26645.188 Da / Num. of mol.: 2 / Fragment: UNP residues 27-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurihydrogenibium azorense (bacteria)
Gene: SULAZ_0541 / Production host: Escherichia coli (E. coli) / References: UniProt: C1DTU5, 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: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: polyethylene glycol monomethyl ether 550, Magnesium chloride, HEPES
PH range: 7.5

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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: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 31032 / % possible obs: 86.9 % / Redundancy: 4.9 % / Rsym value: 0.07 / Net I/σ(I): 19.8
Reflection shellHighest resolution: 1.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 4.15 / % possible all: 70.2

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g7a

4g7a


Resolution: 1.95→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2145 1476 4.1 %
Rwork0.1873 28392 -
obs-29868 83.7 %
Solvent computationBsol: 50.5032 Å2
Displacement parametersBiso max: 56.54 Å2 / Biso mean: 22.4262 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1--6.052 Å2-0 Å20 Å2
2--7.085 Å20 Å2
3----1.033 Å2
Refinement stepCycle: final / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 78 273 3983
Biso mean--31.01 29.06 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.431
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_scbond_it1.9532
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scangle_it2.8932.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.29811040.23292117X-RAY DIFFRACTION63.1
2.02-2.10.2641050.22092276X-RAY DIFFRACTION68.1
2.1-2.20.22831170.20222422X-RAY DIFFRACTION72.4
2.2-2.310.23031510.19662581X-RAY DIFFRACTION77.2
2.31-2.460.22311500.1932719X-RAY DIFFRACTION81.4
2.46-2.650.21891760.18812913X-RAY DIFFRACTION87.2
2.65-2.910.21731540.19213179X-RAY DIFFRACTION93.2
2.91-3.330.22981790.18943266X-RAY DIFFRACTION96.5
3.33-4.20.16861660.16793381X-RAY DIFFRACTION97.8
4.2-200.21271740.18083538X-RAY DIFFRACTION98
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6azm2.param
X-RAY DIFFRACTION7p34.par

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