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- PDB-3cyu: Human Carbonic Anhydrase II complexed with Cryptophane biosensor ... -

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Basic information

Entry
Database: PDB / ID: 3cyu
TitleHuman Carbonic Anhydrase II complexed with Cryptophane biosensor and xenon
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Zinc metalloenzyme / sulfonamide / cryptophane / xenon / biosensor / Disease mutation / Metal-binding
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 / morphogenesis of an epithelium ...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 / 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 / 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
Chem-0CR / Chem-1CR / XENON / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAaron, J.A. / Jude, K.M. / Di Costanzo, L. / Christianson, D.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II.
Authors: Aaron, J.A. / Chambers, J.M. / Jude, K.M. / Di Costanzo, L. / Dmochowski, I.J. / Christianson, D.W.
History
DepositionApr 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4646
Polymers29,2891
Non-polymers3,1755
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.441, 49.985, 81.038
Angle α, β, γ (deg.)90.00, 107.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29289.062 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

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-0CR / MoMo-2-[4-(2-(4-(methoxy)-1H-1,2,3-triazol-1-yl)ethyl)benzenesulfonamide]-7,12-bis-[3-(4-(methoxy)-1H-1,2,3-triazol-1-y l)propanoic acid]-cryptophane-A / 3,3'-{[14,21,28-trimethoxy-42-({1-[2-(4-sulfamoylphenyl)ethyl]-1H-1,2,3-triazol-4-yl}methoxy)-9,12,30,33,43,46-hexaoxad ecacyclo[20.20.4.3~8,37~.3~16,29~.1~13,17~.1~34,38~.0~3,40~.0~5,49~.0~19,24~.0~26,52~]tetrapentaconta-1(42),2,5,7,13(54) ,14,16,19,21,23,26,28,34(47),35,37,40,49,51-octadecaene-7,35-diyl]bis(oxymethanediyl-1H-1,2,3-triazole-4,1-diyl)}dipropa noic acid


Mass: 1423.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C74H74N10O18S
#4: Chemical ChemComp-1CR / PoPo-2-[4-(2-(4-(methoxy)-1H-1,2,3-triazol-1-yl)ethyl)benzenesulfonamide]-7,12-bis-[3-(4-(methoxy)-1H-1,2,3-triazol-1-yl)propanoic acid]-cryptophane-A / 3,3'-{[14,21,28-trimethoxy-42-({1-[2-(4-sulfamoylphenyl)ethyl]-1H-1,2,3-triazol-4-yl}methoxy)-9,12,30,33,43,46-hexaoxadecacyclo[20.20.4.3~8,37~.3~16,29~.1~13,17~.1~34,38~.0~3,40~.0~5,49~.0~19,24~.0~26,52~]tetrapentaconta-1(42),2,5,7,13(54),14,16,19,21,23,26,28,34(47),35,37,40,49,51-octadecaene-7,35-diyl]bis(oxymethanediyl-1H-1,2,3-triazole-4,1-diyl)}dipropanoic acid


Mass: 1423.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C74H74N10O18S
#5: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27-32% PEG 3350, 0.05M Tris-sulfate, 3.5mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2007
RadiationMonochromator: double-bounce downward / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→38.72 Å / Num. all: 27728 / Num. obs: 27728 / % possible obs: 97 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2556 / % possible all: 90.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LG6

1lg6


Resolution: 1.7→38.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 85750.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1139 4.4 %RANDOM
Rwork0.226 ---
obs0.226 25870 90.6 %-
all-27728 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2781 Å2 / ksol: 0.378553 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1--10.41 Å20 Å2-0.95 Å2
2--18.1 Å20 Å2
3----7.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 1.7→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 209 185 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 6
Num. reflection% reflection
Rwork3377 -
obs2556 90.3 %
Rfree-4.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramcre.top
X-RAY DIFFRACTION3water_rep.paramcrx.top
X-RAY DIFFRACTION4cre.par
X-RAY DIFFRACTION5crx.par

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