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- PDB-5jes: Human carbonic anhydrase II (V121T) complexed with benzo[d]thiazo... -

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Basic information

Entry
Database: PDB / ID: 5jes
TitleHuman carbonic anhydrase II (V121T) 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
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: 1.205 Å
AuthorsFox, J.M. / Kang, K. / Sastry, M. / Sherman, W. / Sankaran, B. / Zwart, P.H. / Whitesides, G.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1152196 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
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 18, 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 20, 2017Group: Author supporting evidence / Structure summary / Category: pdbx_audit_support / struct_keywords
Item: _pdbx_audit_support.funding_organization / _struct_keywords.pdbx_keywords
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5674
Polymers29,0731
Non-polymers4943
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.080, 41.280, 72.050
Angle α, β, γ (deg.)90.00, 104.41, 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: 29072.758 Da / Num. of mol.: 1 / Mutation: V121T
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn / References: carbonic anhydrase
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: We soaked monoclinic crystals of HCAII with BTA (EVF) 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 ...Details: We soaked monoclinic crystals of HCAII with BTA (EVF) 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: 1.205→34.892 Å / Num. obs: 117955 / % possible obs: 81.25 % / Redundancy: 3.2 % / Net I/σ(I): 12.6

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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: 1.205→34.892 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1466 3682 3.12 %
Rwork0.1209 --
obs0.1217 117955 81.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.205→34.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 27 374 2459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012246
X-RAY DIFFRACTIONf_angle_d1.7743074
X-RAY DIFFRACTIONf_dihedral_angle_d12.903821
X-RAY DIFFRACTIONf_chiral_restr0.189318
X-RAY DIFFRACTIONf_plane_restr0.007394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2046-1.22050.2679440.21361438X-RAY DIFFRACTION27
1.2205-1.23720.2411620.21791940X-RAY DIFFRACTION35
1.2372-1.25490.2403690.20172246X-RAY DIFFRACTION42
1.2549-1.27360.2316810.1922553X-RAY DIFFRACTION47
1.2736-1.29350.18671100.17372831X-RAY DIFFRACTION53
1.2935-1.31470.2141020.16463305X-RAY DIFFRACTION61
1.3147-1.33740.19491530.16123765X-RAY DIFFRACTION70
1.3374-1.36170.18871160.14814084X-RAY DIFFRACTION75
1.3617-1.38790.20121220.1434368X-RAY DIFFRACTION81
1.3879-1.41620.18861670.13054546X-RAY DIFFRACTION85
1.4162-1.4470.17431520.12114876X-RAY DIFFRACTION90
1.447-1.48070.16541500.1185203X-RAY DIFFRACTION96
1.4807-1.51770.13811830.11255186X-RAY DIFFRACTION96
1.5177-1.55880.14141650.11375151X-RAY DIFFRACTION96
1.5588-1.60460.13711580.10955226X-RAY DIFFRACTION96
1.6046-1.65640.17321580.10985213X-RAY DIFFRACTION96
1.6564-1.71560.13171620.10735252X-RAY DIFFRACTION96
1.7156-1.78430.14651650.10935152X-RAY DIFFRACTION96
1.7843-1.86550.12461800.10975191X-RAY DIFFRACTION96
1.8655-1.96390.17091730.10785242X-RAY DIFFRACTION96
1.9639-2.08690.14911490.115164X-RAY DIFFRACTION96
2.0869-2.2480.14641740.10695238X-RAY DIFFRACTION96
2.248-2.47420.12491650.11825247X-RAY DIFFRACTION97
2.4742-2.8320.12741840.12495225X-RAY DIFFRACTION97
2.832-3.56750.14261610.12655277X-RAY DIFFRACTION98
3.5675-34.90630.13491770.12055354X-RAY DIFFRACTION99

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