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- PDB-5jg3: Human carbonic anhydrase II (121T/N67Q) complexed with benzo[d]th... -

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Basic information

Entry
Database: PDB / ID: 5jg3
TitleHuman carbonic anhydrase II (121T/N67Q) complexed with benzo[d]thiazole-2-sulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Anhydrase / Mutant / Hydrophobic
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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
1,3-benzothiazole-2-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsFox, J.M. / Kang, K. / Sastry, M. / Sherman, W. / Sankaran, B. / Zwart, P.H. / Whitesides, G.M.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase.
Authors: Fox, J.M. / Kang, K. / Sastry, M. / Sherman, W. / Sankaran, B. / Zwart, P.H. / Whitesides, G.M.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6524
Polymers29,1581
Non-polymers4943
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.470, 41.690, 73.080
Angle α, β, γ (deg.)90.00, 104.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29157.863 Da / Num. of mol.: 1 / Mutation: V121T, N67Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-EVF / 1,3-benzothiazole-2-sulfonamide


Mass: 214.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H6N2O2S2 / Details: 1,3-benzothiazole-2-sulfonamide
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn / References: carbonic anhydrase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: We soaked monoclinic crystals of HCAII with BTA and TA by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl ...Details: We soaked monoclinic crystals of HCAII with BTA and TA by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), and 5 mM ligand. (ii) We combined 4 uL of soaking solution and 1-2 crystals of HCAII within a drop on the surface of a reservoir cover (EasyXtal CrystalSupport, Qiagen). (iii) To a clear plastic reservoir in a 15-reservoir plate (EasyXtal, Qiagen), we added 1 mL of soaking solution (without ligand present). We attached the reservoir cover to the reservoir and left the entire setup at 4 deg C for 1 week.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.21→35.908 Å / Num. obs: 135627 / % possible obs: 91.69 % / Redundancy: 3.7 % / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S73

3s73


Resolution: 1.21→35.908 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.83
RfactorNum. reflection% reflection
Rfree0.1517 3709 2.73 %
Rwork0.1318 --
obs0.1323 135627 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.21→35.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 1 417 2508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012302
X-RAY DIFFRACTIONf_angle_d1.3353168
X-RAY DIFFRACTIONf_dihedral_angle_d14.16868
X-RAY DIFFRACTIONf_chiral_restr0.089324
X-RAY DIFFRACTIONf_plane_restr0.007414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.22590.2438940.24753210X-RAY DIFFRACTION58
1.2259-1.24270.2531980.23763653X-RAY DIFFRACTION66
1.2427-1.26050.2711210.22864113X-RAY DIFFRACTION74
1.2605-1.27930.22691340.20724688X-RAY DIFFRACTION85
1.2793-1.29930.22351420.20525001X-RAY DIFFRACTION90
1.2993-1.32060.23891450.1815060X-RAY DIFFRACTION91
1.3206-1.34340.20021330.16655011X-RAY DIFFRACTION92
1.3434-1.36780.18341500.15465206X-RAY DIFFRACTION93
1.3678-1.39410.20661410.14675187X-RAY DIFFRACTION94
1.3941-1.42260.1791470.14345257X-RAY DIFFRACTION94
1.4226-1.45350.15071440.14165213X-RAY DIFFRACTION94
1.4535-1.48730.17511540.12995192X-RAY DIFFRACTION94
1.4873-1.52450.14371540.12175301X-RAY DIFFRACTION95
1.5245-1.56570.14851310.11365259X-RAY DIFFRACTION95
1.5657-1.61180.13971580.11175305X-RAY DIFFRACTION95
1.6118-1.66380.1421350.11335290X-RAY DIFFRACTION96
1.6638-1.72330.16721440.11275301X-RAY DIFFRACTION96
1.7233-1.79230.15261510.11495360X-RAY DIFFRACTION96
1.7923-1.87390.14071410.11625341X-RAY DIFFRACTION97
1.8739-1.97260.14891720.13175334X-RAY DIFFRACTION96
1.9726-2.09620.1431460.11045396X-RAY DIFFRACTION97
2.0962-2.25810.15371590.12725318X-RAY DIFFRACTION97
2.2581-2.48520.14621530.12235446X-RAY DIFFRACTION98
2.4852-2.84470.11241540.1275485X-RAY DIFFRACTION99
2.8447-3.58350.14371540.12495478X-RAY DIFFRACTION99
3.5835-35.92390.12471540.12655513X-RAY DIFFRACTION100

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