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- PDB-4dz9: hCA II in complex with novel sulfonamide inhibitors Set D -

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Basic information

Entry
Database: PDB / ID: 4dz9
TitlehCA II in complex with novel sulfonamide inhibitors Set D
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / mixed a/b globular protein / interconversion of CO2 and bicarbonate / 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 / arylesterase activity / regulation of chloride transport / angiotensin-activated signaling pathway / Reversible hydration of carbon dioxide ...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 / angiotensin-activated signaling pathway / Reversible hydration of carbon dioxide / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / hydro-lyase activity / 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 / apical part of cell / one-carbon metabolic process / 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-ID4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsAggarwal, M. / McKenna, R.
CitationJournal: To be Published
Title: hCA II in complex with novel sulfonamide inhibitors Set D
Authors: Aggarwal, M. / McKenna, R.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 27, 2013ID: 3P29
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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)29,8254
Polymers29,2891
Non-polymers5363
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.250, 41.304, 72.006
Angle α, β, γ (deg.)90.00, 104.09, 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ID4 / 4-[4-(cyclohexylmethyl)-1H-1,2,3-triazol-1-yl]-2,3,5,6-tetrafluorobenzenesulfonamide


Mass: 392.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16F4N4O2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.6M Na-Citrate and 50 mM Tris-Cl at pH 7.8 used as precipitant solution. DMSO was used to dissolve the inhibitor, 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 27, 2010
RadiationMonochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. all: 39670 / Num. obs: 37765 / % possible obs: 95.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 37.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.49-1.544.50.174188.2
1.54-1.614.60.14192.8
1.61-1.684.70.113193.8
1.68-1.774.70.093194.5
1.77-1.884.70.073195.1
1.88-2.024.70.056196.1
2.02-2.234.70.049196.9
2.23-2.554.70.045197.8
2.55-3.214.70.041198.7
3.21-504.60.041198.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KS3

3ks3


Resolution: 1.491→23.864 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.45 / σ(F): 1.34 / Phase error: 15.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 1873 4.96 %
Rwork0.1633 --
obs0.1645 37749 95.44 %
all-39670 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.084 Å2 / ksol: 0.418 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4915 Å20 Å2-0.4284 Å2
2---1.3432 Å20 Å2
3---1.8347 Å2
Refinement stepCycle: LAST / Resolution: 1.491→23.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 31 184 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092162
X-RAY DIFFRACTIONf_angle_d1.3872940
X-RAY DIFFRACTIONf_dihedral_angle_d14.551798
X-RAY DIFFRACTIONf_chiral_restr0.084306
X-RAY DIFFRACTIONf_plane_restr0.007378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.491-1.53130.39321270.39192580X-RAY DIFFRACTION89
1.5313-1.57640.34961380.30422639X-RAY DIFFRACTION92
1.5764-1.62720.25761480.22822692X-RAY DIFFRACTION93
1.6272-1.68540.20011370.17152693X-RAY DIFFRACTION94
1.6854-1.75280.19641430.1552705X-RAY DIFFRACTION95
1.7528-1.83260.18051490.13662710X-RAY DIFFRACTION95
1.8326-1.92920.18781360.13982777X-RAY DIFFRACTION96
1.9292-2.050.16491460.14362773X-RAY DIFFRACTION96
2.05-2.20810.16941470.14432785X-RAY DIFFRACTION97
2.2081-2.43020.1641480.14282830X-RAY DIFFRACTION98
2.4302-2.78140.17321510.15012856X-RAY DIFFRACTION98
2.7814-3.50240.15691510.15972886X-RAY DIFFRACTION99
3.5024-23.86660.20261520.16822950X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -9.4104 Å / Origin y: -1.7905 Å / Origin z: 16.0042 Å
111213212223313233
T0.0632 Å2-0.0017 Å2-0.0007 Å2-0.0599 Å20.0006 Å2--0.0702 Å2
L0.4548 °2-0.0914 °2-0.0203 °2-0.3468 °2-0.0137 °2--0.4724 °2
S0.0046 Å °-0.0314 Å °0.0059 Å °-0.0142 Å °-0.0005 Å °-0.0008 Å °0.008 Å °0.0169 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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