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- PDB-6yh9: Crystal structure of chimeric carbonic anhydrase XII with 2,3,6-t... -

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Basic information

Entry
Database: PDB / ID: 6yh9
TitleCrystal structure of chimeric carbonic anhydrase XII with 2,3,6-trifluoro-5-{[(1R,2S)-2-hydroxy-1,2-diphenylethyl]amino}-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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, 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
Similarity search - Domain/homology
Chem-WWX / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Chemistryopen / Year: 2021
Title: Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII.
Authors: Smirnoviene, J. / Smirnov, A. / Zaksauskas, A. / Zubriene, A. / Petrauskas, V. / Mickeviciute, A. / Michailoviene, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Baranauskiene, L. / ...Authors: Smirnoviene, J. / Smirnov, A. / Zaksauskas, A. / Zubriene, A. / Petrauskas, V. / Mickeviciute, A. / Michailoviene, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Baranauskiene, L. / Chen, W.Y. / Ladbury, J.E. / Matulis, D.
History
DepositionMar 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: 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 24, 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)29,8173
Polymers29,2211
Non-polymers5962
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.734, 40.869, 70.920
Angle α, β, γ (deg.)90.000, 103.340, 90.000
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: 29220.879 Da / Num. of mol.: 1 / Mutation: A65S, N67K, I91T, F130A, V134S, L203N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-WWX / 2,3,6-trifluoro-5-{[(1R,2S)-2-hydroxy-1,2-diphenylethyl]amino}-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 530.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21F3N2O6S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826607 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826607 Å / Relative weight: 1
ReflectionResolution: 1.55→69.01 Å / Num. all: 33601 / Num. obs: 33601 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Rsym value: 0.06 / Net I/av σ(I): 8.3 / Net I/σ(I): 18.3 / Num. measured all: 226751
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.55-1.636.80.3762.13314348690.1670.4410.3764.598.8
1.63-1.736.40.2652.92954745870.1210.3130.2656.198.5
1.73-1.8570.184.23041543530.0780.2090.189.399
1.85-26.80.1186.32748340430.0520.1380.11813.898.6
2-2.196.60.0838.62444837080.0370.0960.08319.598.8
2.19-2.4570.06910.12371134070.030.0790.06924.399.2
2.45-2.836.60.05811.51974829770.0250.0660.05828.798.4
2.83-3.4770.04813.31783425460.020.0540.04837.799.5
3.47-4.96.60.038171312719870.0160.0420.03842.799
4.9-69.0076.50.03516.7729511240.0160.040.03543.498.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
SCALA3.2.19data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q09

4q09


Resolution: 1.55→40.62 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2076 / WRfactor Rwork: 0.1677 / FOM work R set: 0.8683 / SU R Cruickshank DPI: 0.0878 / SU Rfree: 0.0902 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 3386 10.1 %RANDOM
Rwork0.166 ---
obs0.1698 30202 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.29 Å2 / Biso mean: 21.023 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20.42 Å2
2---1.29 Å20 Å2
3---2.14 Å2
Refinement stepCycle: final / Resolution: 1.55→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 36 202 2263
Biso mean--27.57 30.89 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122128
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.662897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73523.689103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72615338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.21157
X-RAY DIFFRACTIONr_chiral_restr0.1280.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021657
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 245 -
Rwork0.233 2212 -
all-2457 -
obs--98.87 %

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