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- PDB-4fik: Human carbonic anhydrase II H64A complexed with thioxolone hydrol... -

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Basic information

Entry
Database: PDB / ID: 4fik
TitleHuman carbonic anhydrase II H64A complexed with thioxolone hydrolysis products
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE II / HUMAN CARBONIC ANHYDRASE II / HCA II / HCA2 / CA II / CA2 / CARBONATE DEHYDRATASE II / CARBONIC ANHYDRASE C / THIOXOLONE / 4-MERCAPTOBENZENE-1 / 3-DIOL / 4-(2 / 4-DIHYDROXYPHENYL) DISULFANYLBENZENE-1 / 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
4,4'-disulfanediyldibenzene-1,3-diol / 4-MERCAPTOBENZENE-1,3-DIOL / 2,4-dihydroxybenzenesulfenic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å
AuthorsSippel, K.H. / Genis, C. / Govindasamy, L. / Agbandje-McKenna, M. / Tripp, B.C. / McKenna, R.
Citation
Journal: J Phys Chem Lett / Year: 2010
Title: Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II.
Authors: Sippel, K.H. / Genis, C. / Govindasamy, L. / Agbandje-McKenna, M. / Kiddle, J.J. / Tripp, B.C. / McKenna, R.
#1: Journal: Biochemistry / Year: 2008
Title: Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study
Authors: Barrese, A.A. / Genis, C. / Fisher, S.Z. / Orwenyo, J.N. / Kumara, M.T. / Dutta, S.K. / Phillips, E. / Kiddle, J.J. / Tu, C. / Silverman, D.N. / Govindasamy, L. / Agbandje-McKenna, M. / McKenna, R. / Tripp, B.C.
History
DepositionJun 8, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJun 27, 2012ID: 3IQK
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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)30,2008
Polymers29,2221
Non-polymers9787
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.370, 41.380, 72.060
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29221.992 Da / Num. of mol.: 1 / Mutation: H64A
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)PLYSS / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 7 types, 306 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TH7 / 2,4-dihydroxybenzenesulfenic acid / 4-HYDROXYSULFANYLBENZENE-1,3-DIOL


Mass: 158.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O3S
#4: Chemical ChemComp-TH0 / 4-MERCAPTOBENZENE-1,3-DIOL


Mass: 142.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2S
#5: Chemical ChemComp-D2S / 4,4'-disulfanediyldibenzene-1,3-diol / 4-(2,4-dihydroxyphenyl)disulfanylbenzene-1,3-diol


Mass: 282.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O4S2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50MM TRIS-HCL, 2.6M AMMONIUM SULFATE, 2UL OF 100UM THIOXOLONE ADDED TO DROP 24HRS PRIOR TO FREEZING, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.938 / Wavelength: 0.938 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2006 / Details: MIRRORS
RadiationMonochromator: HORIZONTAL BENT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.938 Å / Relative weight: 1
ReflectionResolution: 1.2→19.96 Å / Num. all: 75775 / Num. obs: 70016 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 8.36 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.7
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.7 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.5_2)refinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1G0F

1g0f


Resolution: 1.2→15.643 Å / SU ML: 0.08
Isotropic thermal model: Anisotropic for all full occupancy atoms
Cross valid method: THROUGHOUT / σ(F): 0.03 / σ(I): 0 / Phase error: 11.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1374 3369 5.02 %Random
Rwork0.1158 ---
obs0.1168 67156 88.46 %-
all-67156 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso mean: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.2→15.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 58 299 2401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122294
X-RAY DIFFRACTIONf_angle_d1.513162
X-RAY DIFFRACTIONf_dihedral_angle_d19.356869
X-RAY DIFFRACTIONf_chiral_restr0.087323
X-RAY DIFFRACTIONf_plane_restr0.009406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1998-1.24260.18212720.17664845X-RAY DIFFRACTION68
1.2426-1.29240.19372620.15285456X-RAY DIFFRACTION75
1.2924-1.35110.17123190.13646071X-RAY DIFFRACTION85
1.3511-1.42230.16213520.1166430X-RAY DIFFRACTION90
1.4223-1.51140.13593380.09946656X-RAY DIFFRACTION92
1.5114-1.6280.11833500.08996742X-RAY DIFFRACTION94
1.628-1.79160.12023920.0886831X-RAY DIFFRACTION95
1.7916-2.05030.11363660.08937005X-RAY DIFFRACTION97
2.0503-2.58130.12053810.09767004X-RAY DIFFRACTION97
2.5813-15.64460.14473370.13836747X-RAY DIFFRACTION91

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