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- PDB-5t75: Human carbonic anhydrase II G132C_C206S double mutant in complex ... -

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Basic information

Entry
Database: PDB / ID: 5t75
TitleHuman carbonic anhydrase II G132C_C206S double mutant in complex with SA-2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / photopharmacology / carbonic anhydrase / photochromic tethered ligand / azobenzene / computational screening
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 / 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
4-[(E)-(4-aminophenyl)diazenyl]benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDuBay, K.H. / Iwan, K. / Osorio-Planes, L. / Geissler, P. / Groll, M. / Trauner, D. / Broichhagen, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: A Predictive Approach for the Optical Control of Carbonic Anhydrase II Activity.
Authors: DuBay, K.H. / Iwan, K. / Osorio-Planes, L. / Geissler, P.L. / Groll, M. / Trauner, D. / Broichhagen, J.
History
DepositionSep 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: 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
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)29,9374
Polymers29,3191
Non-polymers6183
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.530, 41.480, 72.340
Angle α, β, γ (deg.)90.00, 104.25, 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: 29319.090 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) / 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-4WA / 4-[(E)-(4-aminophenyl)diazenyl]benzenesulfonamide


Mass: 276.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N4O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3 M (NH4)2SO4, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. obs: 37834 / % possible obs: 95.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 1.5→1.6 Å / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.2 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VVA

2vva


Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.979 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17502 1891 5 %RANDOM
Rwork0.14487 ---
obs0.14637 35921 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20.34 Å2
2---0.3 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 31 250 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192147
X-RAY DIFFRACTIONr_bond_other_d0.0020.022012
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9642915
X-RAY DIFFRACTIONr_angle_other_deg1.26734659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4075256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53724.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68415353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.963157
X-RAY DIFFRACTIONr_chiral_restr0.130.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
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_it0.9591.41027
X-RAY DIFFRACTIONr_mcbond_other0.9451.3981026
X-RAY DIFFRACTIONr_mcangle_it1.1972.11282
X-RAY DIFFRACTIONr_mcangle_other1.2032.1031283
X-RAY DIFFRACTIONr_scbond_it1.2831.661120
X-RAY DIFFRACTIONr_scbond_other1.2841.6611121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2952.3751634
X-RAY DIFFRACTIONr_long_range_B_refined2.1517.6392369
X-RAY DIFFRACTIONr_long_range_B_other1.85117.2022331
X-RAY DIFFRACTIONr_rigid_bond_restr1.07634156
X-RAY DIFFRACTIONr_sphericity_free20.1065168
X-RAY DIFFRACTIONr_sphericity_bonded5.32954173
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 125 -
Rwork0.296 2385 -
obs--87.79 %

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