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- PDB-5lle: Crystal structure of human carbonic anhydrase isozyme II with 4-(... -

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Basic information

Entry
Database: PDB / ID: 5lle
TitleCrystal structure of human carbonic anhydrase isozyme II with 4-(1-Adamantylamino)-2,3,5,6-tetrafluorobenzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / 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 / 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
Chem-V51 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsManakova, E. / Smirnov, A. / Grazulis, S.
CitationJournal: PeerJ / Year: 2018
Title: Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding.
Authors: Smirnov, A. / Zubriene, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 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)30,1696
Polymers29,2891
Non-polymers8805
Water3,315184
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint6 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.078, 40.963, 71.599
Angle α, β, γ (deg.)90.000, 103.950, 90.000
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: 29289.062 Da / Num. of mol.: 1 / Fragment: human carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 189 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Fragment: 4-(1-Adamantylamino)-2,3,5,6-tetra uorobenzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-V51 / 4-(1-adamantylamino)-2,3,5,6-tetrakis(fluoranyl)benzenesulfonamide


Mass: 378.385 Da / Num. of mol.: 1 / Fragment: Zn / Source method: obtained synthetically / Formula: C16H18F4N2O2S
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Fragment: DMS / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Fragment: MES / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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 Å3/Da / Density % sol: 37.9 % / Mosaicity: 0.63 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization buffer: 2.5M sodium malonate (Ph 7.5) and 0.075M sodium bicine (pH 9)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→14.246 Å / Num. obs: 18840 / % possible obs: 99.6 % / Redundancy: 3 % / Biso Wilson estimate: 15.714 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/av σ(I): 3.611 / Net I/σ(I): 17.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-22.90.390.81100
2-2.122.90.2911.11100
2.12-2.272.90.2171.91100
2.27-2.4530.1762.41100
2.45-2.6930.1492.81100
2.69-330.1133.71100
3-3.4730.0756.4199.9
3.47-4.2530.0597.8199.7
4.25-6.0130.0488.8199.3
6.01-14.2462.80.0597.4190

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.9→14.24 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.1705 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1912 10.2 %RANDOM
Rwork0.1585 ---
obs0.1642 16914 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 66.81 Å2 / Biso mean: 15.436 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.31 Å2
2---0.16 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.9→14.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 48 184 2281
Biso mean--33.69 23.28 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022176
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9712958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1985259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70224.64699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.83157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211661
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 141 -
Rwork0.199 1230 -
all-1371 -
obs--99.85 %

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