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- PDB-3rz1: Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Bin... -

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Basic information

Entry
Database: PDB / ID: 3rz1
TitleFluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the Hydrophobic Wall of Carbonic Anhydrase
ComponentsCarbonic anhydrase 2
KeywordsLYASE / alpha beta
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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
Chem-RZ1 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSnyder, P.W. / Bai, S. / Heroux, A. / Whitesides, G.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase.
Authors: Mecinovic, J. / Snyder, P.W. / Mirica, K.A. / Bai, S. / Mack, E.T. / Kwant, R.L. / Moustakas, D.T. / Heroux, A. / Whitesides, G.M.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7344
Polymers29,1581
Non-polymers5763
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.275, 41.682, 72.334
Angle α, β, γ (deg.)90.000, 104.660, 90.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, 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-RZ1 / N-(2,2,3,3,4,4,5,5,5-nonafluoropentyl)-4-sulfamoylbenzamide


Mass: 432.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9F9N2O3S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8, vapor diffusion, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.51→69.978 Å / Num. obs: 38523

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→35.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.203 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 1908 5 %RANDOM
Rwork0.1269 ---
obs0.1294 38089 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.77 Å2 / Biso mean: 13.549 Å2 / Biso min: 3.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.51→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 32 272 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222210
X-RAY DIFFRACTIONr_angle_refined_deg2.0891.9653023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31624.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.438157
X-RAY DIFFRACTIONr_chiral_restr0.2070.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211714
X-RAY DIFFRACTIONr_mcbond_it2.4981.51322
X-RAY DIFFRACTIONr_mcangle_it3.66622144
X-RAY DIFFRACTIONr_scbond_it5.1713888
X-RAY DIFFRACTIONr_scangle_it7.2854.5873
X-RAY DIFFRACTIONr_rigid_bond_restr2.7232210
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 141 -
Rwork0.177 2588 -
all-2729 -
obs--96.5 %

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