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- PDB-6rjj: Human Carbonic Anhydrase II in complex with fluorinated benzenesu... -

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Basic information

Entry
Database: PDB / ID: 6rjj
TitleHuman Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / complex / CO2 conversion
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 / 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
(4-CARBOXYPHENYL)(CHLORO)MERCURY / beta-D-glucopyranose / alpha-D-glucopyranose / : / 2,3-bis(fluoranyl)benzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.056 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II.
Authors: Glockner, S. / Ngo, K. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionApr 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,1768
Polymers29,8071
Non-polymers1,3707
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-27 kcal/mol
Surface area11540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.391, 41.678, 72.628
Angle α, β, γ (deg.)90.00, 104.56, 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: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P00918, carbonic anhydrase

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Sugars , 2 types, 2 molecules

#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#6: Chemical ChemComp-K5W / 2,3-bis(fluoranyl)benzenesulfonamide


Mass: 193.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5F2NO2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2017
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.056→41.678 Å / Num. obs: 109461 / % possible obs: 97.3 % / Redundancy: 3.67 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.999 / Rsym value: 0.051 / Net I/σ(I): 12.46
Reflection shellResolution: 1.06→1.12 Å / Redundancy: 3.64 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 17106 / CC1/2: 0.842 / Rsym value: 0.53 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.056→41.03 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.12
RfactorNum. reflection% reflectionSelection details
Rfree0.1381 5473 5 %Random selection of 5 %
Rwork0.1226 ---
obs0.1234 109451 97.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.056→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 60 259 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092546
X-RAY DIFFRACTIONf_angle_d1.1113519
X-RAY DIFFRACTIONf_dihedral_angle_d17.846953
X-RAY DIFFRACTIONf_chiral_restr0.094367
X-RAY DIFFRACTIONf_plane_restr0.008491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0563-1.06830.43491530.43552911X-RAY DIFFRACTION82
1.0683-1.08090.29291820.30093458X-RAY DIFFRACTION97
1.0809-1.09410.25671820.22923452X-RAY DIFFRACTION97
1.0941-1.10790.18841790.19683415X-RAY DIFFRACTION97
1.1079-1.12250.19771830.17273475X-RAY DIFFRACTION98
1.1225-1.13790.17291830.16013458X-RAY DIFFRACTION98
1.1379-1.15420.17251830.16183485X-RAY DIFFRACTION98
1.1542-1.17140.17811800.16243414X-RAY DIFFRACTION97
1.1714-1.18970.14291800.13333430X-RAY DIFFRACTION96
1.1897-1.20920.13361830.11363466X-RAY DIFFRACTION98
1.2092-1.23010.12211830.10233480X-RAY DIFFRACTION98
1.2301-1.25240.12681830.09863484X-RAY DIFFRACTION98
1.2524-1.27650.10641830.09943481X-RAY DIFFRACTION98
1.2765-1.30260.12261850.09493501X-RAY DIFFRACTION98
1.3026-1.33090.11681840.09043510X-RAY DIFFRACTION99
1.3309-1.36190.10921830.09373477X-RAY DIFFRACTION99
1.3619-1.39590.12541860.09413520X-RAY DIFFRACTION98
1.3959-1.43370.12531810.09593437X-RAY DIFFRACTION97
1.4337-1.47590.12511820.0913475X-RAY DIFFRACTION98
1.4759-1.52350.11971870.09653549X-RAY DIFFRACTION99
1.5235-1.57790.10741840.09663502X-RAY DIFFRACTION99
1.5779-1.64110.13081860.09853516X-RAY DIFFRACTION98
1.6411-1.71580.1161830.10323476X-RAY DIFFRACTION98
1.7158-1.80630.12621840.10713515X-RAY DIFFRACTION98
1.8063-1.91940.11481830.10853473X-RAY DIFFRACTION97
1.9194-2.06760.12331810.11373434X-RAY DIFFRACTION96
2.0676-2.27570.12321860.11453529X-RAY DIFFRACTION99
2.2757-2.6050.13591870.12643551X-RAY DIFFRACTION98
2.605-3.28180.16521850.14243527X-RAY DIFFRACTION98
3.2818-41.06130.14111890.13363577X-RAY DIFFRACTION97

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