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- PDB-5w8b: Carbonic anhydrase II in complex with activating histamine pyridi... -

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Basic information

Entry
Database: PDB / ID: 5w8b
TitleCarbonic anhydrase II in complex with activating histamine pyridinium derivative
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Complex / Activator / Ligand
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 / regulation of intracellular pH / morphogenesis of an epithelium / 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
Chem-A57 / Hexafluorophosphate anion / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.601 Å
AuthorsBhatt, A. / Ilies, M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109524 United States
CitationJournal: Mol. Neurobiol. / Year: 2018
Title: Crystal Structure of Carbonic Anhydrase II in Complex with an Activating Ligand: Implications in Neuronal Function.
Authors: Bhatt, A. / Mondal, U.K. / Supuran, C.T. / Ilies, M.A. / McKenna, R.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,5085
Polymers28,9331
Non-polymers5754
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.268, 41.252, 72.096
Angle α, β, γ (deg.)90.000, 104.100, 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 / Fragment: UNP residues 4-260
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, 155 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A9J / Hexafluorophosphate anion


Mass: 144.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A57 / 1-[2-(1H-imidazol-5-yl)ethyl]-4-methyl-2,6-di(propan-2-yl)pyridin-1-ium


Mass: 272.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 1.4M Sodium Citrate, 50mM Tris, pH 7.8
Temp details: Tray stored in styrofoam box at room temperature.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryosystems cryocooler
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2016
Details: White beam collimating mirror, horizontally focusing monochromator using single bent triangular Si(111) crystal, vertically focusing Rh-coated Si mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→40.995 Å / Num. obs: 54244 / % possible obs: 98.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Χ2: 1.051 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.80.5510.8590.2480.6070.94598.9
1.63-1.665.80.4990.8550.2260.550.997.6
1.66-1.695.90.4270.9030.190.4690.87997.2
1.69-1.726.20.3640.9260.1590.3990.86399.2
1.72-1.766.30.3240.9450.1390.3540.90499.1
1.76-1.86.30.2710.9580.1160.2950.91398.4
1.8-1.856.20.220.970.0940.240.87697.5
1.85-1.96.10.190.9750.0820.2080.90997.9
1.9-1.955.90.1580.9790.070.1730.91896.5
1.95-2.0260.1330.9880.0580.1460.91196.8
2.02-2.096.30.1180.990.050.1290.9397.1
2.09-2.176.40.10.9910.0430.1090.91697.4
2.17-2.276.40.090.9920.0380.0970.95596.6
2.27-2.396.20.0880.9930.0370.0961.20297.9
2.39-2.545.90.0730.9950.0320.080.94898.1
2.54-2.746.10.0650.9950.0280.0710.90298.4
2.74-3.016.50.0630.9960.0260.0691.08899.2
3.01-3.456.50.0590.9950.0250.0641.399.5
3.45-4.346.40.0630.9960.0260.0681.51699.2
4.34-206.50.0630.9960.0260.0692.00199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10pre_2097refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.601→40.995 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.1832 1560 4.99 %
Rwork0.1559 --
obs0.1573 54244 87.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.23 Å2 / Biso mean: 17.085 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: final / Resolution: 1.601→40.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 106 151 2306
Biso mean--38.58 23.61 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072180
X-RAY DIFFRACTIONf_angle_d1.2832950
X-RAY DIFFRACTIONf_chiral_restr0.064301
X-RAY DIFFRACTIONf_plane_restr0.007379
X-RAY DIFFRACTIONf_dihedral_angle_d10.6611272
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6012-1.63030.19611030.1905174856
1.6303-1.66170.20181110.1811179559
1.6617-1.69560.217980.1735201664
1.6956-1.73250.20851090.1627223572
1.7325-1.77280.21781290.1624241278
1.7728-1.81710.20871430.1569255683
1.8171-1.86630.14681510.1554269787
1.8663-1.92120.21561500.1611284490
1.9212-1.98320.20081470.1589290594
1.9832-2.05410.19691550.1516297395
2.0541-2.13630.17271610.1491297196
2.1363-2.23350.17271560.1523301896
2.2335-2.35130.17661590.1613299896
2.3513-2.49860.23271450.1647300497
2.4986-2.69140.20231500.1707300897
2.6914-2.96220.19311560.1704309998
2.9622-3.39070.1811650.1571303199
3.3907-4.27120.14661650.1343311399
4.2712-40.9950.16761530.14733115100
Refinement TLS params.Method: refined / Origin x: -9.3394 Å / Origin y: -1.493 Å / Origin z: 15.9359 Å
111213212223313233
T0.0574 Å2-0.0049 Å20.0006 Å2-0.0568 Å2-0.0033 Å2--0.0587 Å2
L0.3296 °2-0.0876 °20.0051 °2-0.2695 °2-0.0614 °2--0.2457 °2
S0.0012 Å °-0.0242 Å °0.015 Å °-0.0178 Å °0.0006 Å °0.0053 Å °0.0043 Å °0.0123 Å °-0.0128 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB1 - 157
3X-RAY DIFFRACTION1allC262
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allE400
6X-RAY DIFFRACTION1allF1

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