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- PDB-4ygn: NaI--Interactions between Hofmeister Anions and the Binding Pocke... -

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Basic information

Entry
Database: PDB / ID: 4ygn
TitleNaI--Interactions between Hofmeister Anions and the Binding Pocket of a Protein
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Hofmeister Anions / HCAII
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / 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
IODIDE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å
AuthorsFox, J.M. / Kang, K. / Sherman, W. / Heroux, A. / Sastry, G.M. / Baghbanzadeh, M. / Lockett, M.R. / Whitesides, G.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1152196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)8P41GM103473-16 United States
Department of Energy (DOE, United States)BO-70 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Interactions between Hofmeister Anions and the Binding Pocket of a Protein.
Authors: Fox, J.M. / Kang, K. / Sherman, W. / Heroux, A. / Sastry, G.M. / Baghbanzadeh, M. / Lockett, M.R. / Whitesides, G.M.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6997
Polymers28,9991
Non-polymers7006
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.341, 41.336, 72.837
Angle α, β, γ (deg.)90.00, 104.57, 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: 28998.656 Da / Num. of mol.: 1 / Fragment: UNP residues 3-260
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: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 59438 / % possible obs: 82.4 % / Redundancy: 2.6 % / Net I/σ(I): 29.7
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 4 / % possible all: 26.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.23→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.584 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20937 3163 5.1 %RANDOM
Rwork0.17525 ---
obs0.17694 59438 87.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.02 Å2
2---0.23 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 6 138 2183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192147
X-RAY DIFFRACTIONr_bond_other_d0.0020.022003
X-RAY DIFFRACTIONr_angle_refined_deg2.1641.952930
X-RAY DIFFRACTIONr_angle_other_deg1.09934648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92624.752101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3715352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.994157
X-RAY DIFFRACTIONr_chiral_restr0.2030.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212447
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02496
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1251.2221042
X-RAY DIFFRACTIONr_mcbond_other1.9941.2191041
X-RAY DIFFRACTIONr_mcangle_it2.3991.841303
X-RAY DIFFRACTIONr_mcangle_other2.4271.8441304
X-RAY DIFFRACTIONr_scbond_it4.0031.5351105
X-RAY DIFFRACTIONr_scbond_other4.0021.5361106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9492.171619
X-RAY DIFFRACTIONr_long_range_B_refined3.52710.5772436
X-RAY DIFFRACTIONr_long_range_B_other3.50910.3962391
X-RAY DIFFRACTIONr_rigid_bond_restr9.61534150
X-RAY DIFFRACTIONr_sphericity_free16.772553
X-RAY DIFFRACTIONr_sphericity_bonded8.36354170
LS refinement shellResolution: 1.23→1.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 94 -
Rwork0.23 1921 -
obs--38.39 %

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