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- PDB-6bc9: Joint X-ray/neutron structure of human carbonic anhydrase II in c... -

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Basic information

Entry
Database: PDB / ID: 6bc9
TitleJoint X-ray/neutron structure of human carbonic anhydrase II in complex with dorzolamide
ComponentsCarbonic anhydrase 2
Keywordslyase/lyase inhibitor / protonation state / drug binding / hydrogen bonding / LYASE / 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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 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
DEUTERATED WATER / Chem-ETS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKovalevsky, A. / McKenna, R. / Aggarwal, M.
Citation
Journal: Structure / Year: 2018
Title: "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation.
Authors: Kovalevsky, A. / Aggarwal, M. / Velazquez, H. / Cuneo, M.J. / Blakeley, M.P. / Weiss, K.L. / Smith, J.C. / Fisher, S.Z. / McKenna, R.
#1: Journal: Acta Cryst. / Year: 2009
Title: Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
Authors: Adams, P.D. / Mustyakimov, M. / Afonine, P.V. / Langan, P.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6793
Polymers29,2891
Non-polymers3902
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.800, 42.100, 72.700
Angle α, β, γ (deg.)90.00, 104.60, 90.00
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: 29289.062 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ETS / (4S-TRANS)-4-(ETHYLAMINO)-5,6-DIHYDRO-6-METHYL-4H-THIENO(2,3-B)THIOPYRAN-2-SULFONAMIDE-7,7-DIOXIDE / Dorzolamide


Mass: 324.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O4S3 / Comment: medication*YM
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate, 50 mM TRIS pH 8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORORNL Spallation Neutron Source MANDI22.0 - 4.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEAug 8, 2016OSMIC VARIMAX
ORNL ANGER CAMERA2AREA DETECTORAug 19, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2neutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
221
341
Reflection

Entry-ID: 6BC9

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.63-403011595.36.10.079118.6
1.8-13.82047889.22.80.145214.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.63-1.665.20.3335183.5
1.8-1.862.20.3244278.8

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Processing

SoftwareName: nCNS / Version: 1.0.0 / Classification: refinement
Refinement

Method to determine structure: MOLECULAR REPLACEMENT

Starting modelResolution (Å)Refine-IDRfactor RfreeRfactor RworkNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)R Free selection detailsCross valid methodσ(F)
5C8I

5c8i

1.8-13.8X-RAY DIFFRACTION0.1960.178148320817588.6RANDOMFREE R-VALUE2.5
NEUTRON DIFFRACTION
Refinement stepCycle: LAST / Resolution: 1.8→13.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 20 123 2192
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 115 5 %
Rwork0.345 2899 -
obs--78.2 %

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