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- PDB-6ql1: Crystal structure of chimeric carbonic anhydrase VI with 4-[(4,6-... -

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Basic information

Entry
Database: PDB / ID: 6ql1
TitleCrystal structure of chimeric carbonic anhydrase VI with 4-[(4,6-dimethylpyrimidin-2-yl)thio]-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 / 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-V50 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Sci Rep / Year: 2019
Title: Engineered Carbonic Anhydrase VI-Mimic Enzyme Switched the Structure and Affinities of Inhibitors.
Authors: Kazokaite, J. / Kairys, V. / Smirnoviene, J. / Smirnov, A. / Manakova, E. / Tolvanen, M. / Parkkila, S. / Matulis, D.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4938
Polymers29,3661
Non-polymers1,1267
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-2 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.299, 41.401, 71.242
Angle α, β, γ (deg.)90.000, 104.310, 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: 29366.055 Da / Num. of mol.: 1 / Fragment: human carbonic anhydrase II / Mutation: A65T, N67Q, F130Y, V134Q, L203T
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 , 7 types, 292 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Fragment: 4-[(4,6-dimethylpyrimidin-2-yl)thio]-2,3,5,6-tetrafluorobenzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Fragment: Dimethyl sulfoxide / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Fragment: 2-(Bis(2-hydroxyethyl)amino)acetic acid / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical ChemComp-V50 / 4-[(4,6-dimethylpyrimidin-2-yl)thio]-2,3,5,6-tetrafluorobenzenesulfonamide


Mass: 367.342 Da / Num. of mol.: 2 / Fragment: ethane-1,2-diol / Source method: obtained synthetically / Formula: C12H9F4N3O2S2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Fragment: Na / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 40.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer was 0.1M sodium BICINE (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)

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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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.418→69.031 Å / Num. all: 42097 / Num. obs: 42097 / % possible obs: 92.8 % / Redundancy: 7 % / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Rsym value: 0.042 / Net I/av σ(I): 9.804 / Net I/σ(I): 22.7 / Num. measured all: 293373
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.42-1.56.60.24130.1120.2930.24174.1
1.5-1.597.10.1624.40.0720.1930.16295
1.59-1.76.90.11660.0530.1410.11694.2
1.7-1.837.20.0828.40.0370.1010.08296.4
1.83-2.016.90.05711.90.0270.0710.05795.1
2.01-2.247.20.04415.20.020.0550.04497.4
2.24-2.596.90.03816.80.0180.0480.03896.2
2.59-3.177.20.03517.40.0160.0430.03598.6
3.17-4.496.80.0317.90.0140.0360.0396.7
4.49-69.0316.80.02918.10.0130.0350.02997.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.42→39.86 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.0725 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 4219 10 %RANDOM
Rwork0.1583 ---
obs0.1611 42082 92.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 87.09 Å2 / Biso mean: 16.7794 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.22 Å2
2---0.12 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.42→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 67 285 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122341
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.6823207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11823.772114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12415377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.978158
X-RAY DIFFRACTIONr_chiral_restr0.1370.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021873
X-RAY DIFFRACTIONr_mcbond_it1.6721.3351111
X-RAY DIFFRACTIONr_mcangle_it2.482.0011415
X-RAY DIFFRACTIONr_scbond_it2.6641.6391230
LS refinement shellResolution: 1.418→1.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 197 -
Rwork0.215 1740 -
all-1937 -
obs--57.7 %

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