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- PDB-5ti0: Crystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bo... -

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Basic information

Entry
Database: PDB / ID: 5ti0
TitleCrystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bound to human carbonic anhydrase 2 L198G
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic Anhydrase 2 / Complex / metalloenzyme inhibitor / LYASE-LYASE INHIBITOR complex
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
2-hydroxycyclohepta-2,4,6-triene-1-thione / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDick, B. / Cohen, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098435 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2017
Title: Effect of donor atom identity on metal-binding pharmacophore coordination.
Authors: Dick, B.L. / Patel, A. / McCammon, J.A. / Cohen, S.M.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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)29,5935
Polymers29,2331
Non-polymers3604
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint8 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.123, 41.136, 71.865
Angle α, β, γ (deg.)90.00, 104.44, 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: 29232.953 Da / Num. of mol.: 1 / Mutation: L198G
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-7CZ / 2-hydroxycyclohepta-2,4,6-triene-1-thione


Mass: 138.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6OS
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Ammonium Sulfate, Tris, pH 8.0 VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5478 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 1.4→69.59 Å / Num. obs: 46899 / % possible obs: 99.8 % / Redundancy: 6.32 % / Rmerge(I) obs: 0.0489 / Net I/σ(I): 14.18
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.5822 / Num. unique all: 1663 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
APEXdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.42→40 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.11 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19574 2261 5 %RANDOM
Rwork0.16272 ---
obs0.16432 42962 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0.07 Å2
2---0.04 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.42→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 18 195 2258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192224
X-RAY DIFFRACTIONr_bond_other_d0.0030.022068
X-RAY DIFFRACTIONr_angle_refined_deg2.3251.953025
X-RAY DIFFRACTIONr_angle_other_deg1.523.0014802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3455272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75224.857105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.57157
X-RAY DIFFRACTIONr_chiral_restr0.1520.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02514
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_it1.5161.081070
X-RAY DIFFRACTIONr_mcbond_other1.4391.0761069
X-RAY DIFFRACTIONr_mcangle_it2.1881.6171348
X-RAY DIFFRACTIONr_mcangle_other2.1911.621349
X-RAY DIFFRACTIONr_scbond_it2.5761.3531154
X-RAY DIFFRACTIONr_scbond_other2.5751.3541155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9171.9121678
X-RAY DIFFRACTIONr_long_range_B_refined4.9519.7782637
X-RAY DIFFRACTIONr_long_range_B_other4.9519.7822638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 182 -
Rwork0.255 3124 -
obs--99.85 %

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