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- PDB-6ouj: Carbonic Anhydrase II complexed with benzene sulfonamide MB11-689A -

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Basic information

Entry
Database: PDB / ID: 6ouj
TitleCarbonic Anhydrase II complexed with benzene sulfonamide MB11-689A
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / benzene sulfonamide / carbonic anhydrase / inhibitor / LYASE / lyase-lyase inhibitor complex
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / Developmental Lineage of Pancreatic Ductal Cells / carbonic anhydrase / carbonate dehydratase activity ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / Developmental Lineage of Pancreatic Ductal Cells / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / regulation of intracellular pH / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / apical part of cell / 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-N7V / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.466 Å
AuthorsKota, A. / McKenna, R.
CitationJournal: To Be Published
Title: Carbonic Anhydrase II complexed with benzene sulfonamide MB11-689A
Authors: Kota, A. / McKenna, R.
History
DepositionMay 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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)29,5325
Polymers28,9331
Non-polymers5994
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.255, 41.178, 71.772
Angle α, β, γ (deg.)90.000, 104.150, 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: 28932.641 Da / Num. of mol.: 1
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 , 5 types, 241 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-N7V / 3-[(1S)-1-(4-nitrophenyl)ethyl]-2-oxo-2,3-dihydro-1,3-benzoxazole-5-sulfonamide


Mass: 363.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3O6S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 41.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.6M sodium citrate, 50mM Tris HCl, pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.4656→25.2944 Å / Num. obs: 39660 / % possible obs: 96 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.86 Å2 / Net I/σ(I): 16.97
Reflection shellResolution: 1.466→1.518 Å / Num. unique obs: 3819

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.466→25.2944 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.51
RfactorNum. reflection% reflection
Rfree0.1808 1901 4.79 %
Rwork0.1564 --
obs0.1576 39657 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.14 Å2 / Biso mean: 19.1195 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: final / Resolution: 1.466→25.2944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 35 240 2324
Biso mean--40.52 32.02 -
Num. residues----257
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.466-1.50220.52461150.4947254492
1.5022-1.54280.36691400.3164262994
1.5428-1.58820.20461170.2075266995
1.5882-1.63950.19721250.1688263794
1.6395-1.69810.19681230.1594264794
1.6981-1.7660.19381250.1541268396
1.766-1.84640.15981650.1558268496
1.8464-1.94370.17861720.1486265597
1.9437-2.06540.15421370.1368270697
2.0654-2.22480.17171080.1394275496
2.2248-2.44850.18641320.1496276098
2.4485-2.80250.17481420.1509275398
2.8025-3.52930.16541550.1378278198
3.5293-25.29440.16231450.1432285498
Refinement TLS params.Method: refined / Origin x: -9.3869 Å / Origin y: -1.6584 Å / Origin z: 15.7939 Å
111213212223313233
T0.0958 Å2-0.003 Å20.0011 Å2-0.0937 Å2-0.0009 Å2--0.0982 Å2
L0.558 °2-0.0954 °20.0374 °2-0.4522 °2-0.0581 °2--0.4726 °2
S-0.0013 Å °-0.0194 Å °0.0212 Å °-0.0247 Å °0.005 Å °-0.0057 Å °0.0109 Å °0.0153 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 313
4X-RAY DIFFRACTION1allE400
5X-RAY DIFFRACTION1allF2
6X-RAY DIFFRACTION1allC1

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