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- PDB-5thi: Crystal Structure of 2-hydroxycyclohepta-2,4,6-trien-1-one bound ... -

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Basic information

Entry
Database: PDB / ID: 5thi
TitleCrystal Structure of 2-hydroxycyclohepta-2,4,6-trien-1-one 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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / cytoplasm / cytosol
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-TRIEN-1-ONE / CITRIC ACID / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDick, B. / Cohen, S.
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 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Oct 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)30,1187
Polymers29,2331
Non-polymers8866
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint4 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.186, 41.368, 71.727
Angle α, β, γ (deg.)90.00, 104.20, 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: 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

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Non-polymers , 6 types, 213 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-0TR / 2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE / TROPOLONE


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 41.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion / 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: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 1.5→69.54 Å / Num. obs: 38528 / % possible obs: 99.5 % / Redundancy: 5.09 % / Rmerge(I) obs: 0.0538 / Net I/σ(I): 12.87
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4379 / Num. unique all: 1376 / % possible all: 90.9

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Processing

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

3ks3


Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.491 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19593 1885 4.9 %RANDOM
Rwork0.16864 ---
obs0.17003 36588 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0.02 Å2
2---0.26 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 45 207 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192263
X-RAY DIFFRACTIONr_bond_other_d0.0040.022084
X-RAY DIFFRACTIONr_angle_refined_deg2.1471.9613082
X-RAY DIFFRACTIONr_angle_other_deg1.5543.0034846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2235278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71724.854103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46815373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.579157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212588
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02518
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_it1.5511.1331085
X-RAY DIFFRACTIONr_mcbond_other1.5321.1291084
X-RAY DIFFRACTIONr_mcangle_it2.3121.6941372
X-RAY DIFFRACTIONr_mcangle_other2.3161.6971373
X-RAY DIFFRACTIONr_scbond_it2.5751.4061178
X-RAY DIFFRACTIONr_scbond_other2.5741.4081179
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8921.9941711
X-RAY DIFFRACTIONr_long_range_B_refined5.15310.2692707
X-RAY DIFFRACTIONr_long_range_B_other5.15210.2782708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 131 -
Rwork0.254 2578 -
obs--95.32 %

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