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- PDB-5c8i: Joint X-ray/neutron structure of Human Carbonic Anhydrase II in c... -

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Basic information

Entry
Database: PDB / ID: 5c8i
TitleJoint X-ray/neutron structure of Human Carbonic Anhydrase II in complex with Methazolamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / methazolamide / acetazolamide / water displacement
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 / arylesterase activity / regulation of chloride transport / 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 / arylesterase activity / regulation of chloride transport / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
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-MZM / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsAggarwal, M. / Kovalevsky, A.Y. / Fisher, S.Z. / McKenna, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)0922719 United States
Oak Ridge National Lab/Shull FellowshipNDSB0001 United States
CitationJournal: IUCrJ / Year: 2016
Title: Neutron structure of human carbonic anhydrase II in complex with methazolamide: mapping the solvent and hydrogen-bonding patterns of an effective clinical drug.
Authors: Aggarwal, M. / Kovalevsky, A.Y. / Velazquez, H. / Fisher, S.Z. / Smith, J.C. / McKenna, R.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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)29,5913
Polymers29,2891
Non-polymers3022
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.893, 41.763, 72.949
Angle α, β, γ (deg.)90.00, 104.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2


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-MZM / N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2(3H)-ylidene)acetamide / Methazolamide


Mass: 236.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N4O3S2 / Comment: inhibitor*YM
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 43.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 1.6M Na-citrate, 50 mM Tris

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU11.54
NUCLEAR REACTORORNL High Flux Isotope Reactor CG4D22.8-4.5
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEJan 15, 2015
MAATEL IMAGINE2IMAGE PLATEJan 30, 2015ELLIPTICAL MIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2neutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
22.81
34.51
Reflection

Entry-ID: 5C8I

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.55-19.063583992.34.70.084116.05
2.2-41.491041780.63.80.17724.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.56-1.594.30.3825.39183.4
2.19-2.313.50.2962.6266

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Processing

Software
NameVersionClassification
nCNS1.0.0refinement
CNSphasing
Refinement

Biso max: 71.49 Å2 / Biso mean: 21.3 Å2 / Biso min: 7.23 Å2 / Cross valid method: FREE R-VALUE / Stereochemistry target values: Joint X-ray/neutron ML / Solvent model: CNS bulk solvent model used

Method to determine structureResolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)R Free selection detailsDiffraction-IDBsol (Å2)ksol (e/Å3)
MOLECULAR REPLACEMENT1.56-19.06X-RAY DIFFRACTION0.2210.0050.20416273018735836318145.188.8RANDOM143.04440.353012
2.2-35.94NEUTRON DIFFRACTION0.2760.0130.2254568737129269193571.12100.391064
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.20.18
Luzzati d res low-5
Luzzati sigma a0.090.08
Luzzati d res high-1.56
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.370.28
Luzzati d res low-5
Luzzati sigma a0.430.39
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 1.56→19.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 15 77 2141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_torsion_deg16.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.92
NEUTRON DIFFRACTIONx_bond_d0.01
NEUTRON DIFFRACTIONx_angle_deg1.1
NEUTRON DIFFRACTIONx_torsion_deg16.2
NEUTRON DIFFRACTIONx_torsion_impr_deg0.92
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.56-1.630.2841835.40.2973178X-RAY DIFFRACTION0.0214426336175.9
1.63-1.720.2572065.60.2473476X-RAY DIFFRACTION0.0184488368282
1.72-1.820.2412025.30.2113642X-RAY DIFFRACTION0.0174463384486.1
1.82-1.970.2342125.40.2013739X-RAY DIFFRACTION0.0164461395188.6
1.97-2.160.2342004.90.2143868X-RAY DIFFRACTION0.0174452406891.4
2.16-2.470.2312074.90.2153992X-RAY DIFFRACTION0.0164499419993.3
2.47-3.120.2242024.70.2144082X-RAY DIFFRACTION0.0164507428495.1
3.12-19.060.1952154.90.1784210X-RAY DIFFRACTION0.0134595442596.3
2.2-2.30.388465.70.335758NEUTRON DIFFRACTION0.057159680450.4
2.3-2.420.319404.50.28851NEUTRON DIFFRACTION0.05159389155.9
2.42-2.570.316505.20.272913NEUTRON DIFFRACTION0.045161496359.7
2.57-2.770.364615.70.2571014NEUTRON DIFFRACTION0.0471606107566.9
2.77-3.050.326504.30.2391100NEUTRON DIFFRACTION0.0461602115071.8
3.05-3.490.251614.50.211284NEUTRON DIFFRACTION0.0321624134582.8
3.49-4.40.23704.80.1761376NEUTRON DIFFRACTION0.0281615144689.5
4.4-35.940.212785.10.1951441NEUTRON DIFFRACTION0.0241684151990.2

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