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- PDB-3v2j: Effect of Sucrose and Glycerol as Cryoprotectans, on the Inhibiti... -

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Basic information

Entry
Database: PDB / ID: 3v2j
TitleEffect of Sucrose and Glycerol as Cryoprotectans, on the Inhibition of Human Carbonic Anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Glycerol / sucrose / cryoprotectant / Acetazolamide / hCA II
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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsAggarwal, M. / McKenna, A.
CitationJournal: To be Published
Title: Effect of Sucrose and Glycerol as Cryoprotectans, on the Inhibition of Human Carbonic Anhydrase II
Authors: Aggarwal, M. / McKenna, A.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,5773
Polymers29,2891
Non-polymers2882
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.811, 41.704, 72.929
Angle α, β, γ (deg.)90.00, 104.49, 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-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Acetazolamide


Mass: 222.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.6M Na-Citrate, 50mM Tris-Cl as precipitant solution. DMSO to dissolve AZM. 10 uL drops of CA II-AZM in 50% precipitant solution, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 26, 2011
RadiationMonochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.699→19.976 Å / Num. obs: 26188

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→19.028 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.28 / σ(F): 1.35 / Phase error: 14.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1666 1307 4.99 %
Rwork0.1396 --
obs0.141 26188 94.55 %
all-27712 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.851 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.699→19.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 14 89 2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092172
X-RAY DIFFRACTIONf_angle_d1.252937
X-RAY DIFFRACTIONf_dihedral_angle_d13.276797
X-RAY DIFFRACTIONf_chiral_restr0.08308
X-RAY DIFFRACTIONf_plane_restr0.007382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6994-1.76740.22461290.19092622X-RAY DIFFRACTION91
1.7674-1.84780.19141420.15422651X-RAY DIFFRACTION92
1.8478-1.94510.17261470.1352707X-RAY DIFFRACTION92
1.9451-2.06680.15041440.11962727X-RAY DIFFRACTION94
2.0668-2.22620.1631460.13192735X-RAY DIFFRACTION94
2.2262-2.44980.17111470.13452789X-RAY DIFFRACTION95
2.4498-2.80340.17791440.15162819X-RAY DIFFRACTION96
2.8034-3.52820.16411520.15072871X-RAY DIFFRACTION97
3.5282-19.02960.15461560.1282960X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47910.27630.23231.5797-0.00122.5551-0.10820.1419-0.3701-0.08130.0102-0.30770.32540.3750.10630.0960.0120.04050.1937-0.02990.23078.509-2.567316.5719
21.1871-0.55410.14241.10.08661.4766-0.0261-0.14890.06920.06260.06390.0625-0.0902-0.1992-0.02950.077-0.01250.00060.09270.00520.0938-13.99892.46818.4431
30.9387-0.00180.04550.7681-0.25611.1042-0.0141-0.0494-0.02080.0774-0.00050.05770.0326-0.04470.02280.0809-0.00830.00410.06960.00140.0834-11.6511-3.713418.4204
41.0297-0.02080.08771.10370.04851.43030.0462-0.04690.11250.0156-0.07980.0466-0.0491-0.00870.02250.0661-0.0031-0.00060.0606-0.00410.0707-11.55434.288218.1805
56.26782.4348-2.28793.1051-1.58273.0537-0.18790.5326-0.2051-0.57960.22410.25190.2154-0.4040.10240.2057-0.0231-0.04250.1618-0.01430.1612-15.9241-6.34930.1725
61.1608-0.12380.09310.9435-0.09681.19560.02250.122-0.0527-0.1188-0.0104-0.01570.111-0.0112-0.00720.0780.00130.00650.06580.00040.069-9.7414-4.859511.7042
73.1704-1.024-0.63691.5490.79760.928-0.1422-0.93980.25560.32250.1421-0.02530.0680.1216-0.06950.19190.00370.01080.23550.00910.0679-9.4183-3.742933.5817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:24)
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:77)
3X-RAY DIFFRACTION3chain 'A' and (resseq 78:115)
4X-RAY DIFFRACTION4chain 'A' and (resseq 116:154)
5X-RAY DIFFRACTION5chain 'A' and (resseq 155:167)
6X-RAY DIFFRACTION6chain 'A' and (resseq 168:248)
7X-RAY DIFFRACTION7chain 'A' and (resseq 249:261)

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