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- PDB-3d93: Apo Human carbonic anhydrase II bound with substrate carbon dioxide -

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Basic information

Entry
Database: PDB / ID: 3d93
TitleApo Human carbonic anhydrase II bound with substrate carbon dioxide
Componentscarbonic anhydrase IICarbonic anhydrase
KeywordsLYASE / zinc metalloenzyme / substrate-bound / Disease mutation / Metal-binding
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 / 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
CARBON DIOXIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsDomsic, J.F. / Avvaru, B.S. / McKenna, R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Entrapment of carbon dioxide in the active site of carbonic anhydrase II
Authors: Domsic, J.F. / Avvaru, B.S. / Kim, C.U. / Gruner, S.M. / Agbandje-McKenna, M. / Silverman, D.N. / McKenna, R.
History
DepositionMay 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: carbonic anhydrase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4694
Polymers29,2891
Non-polymers1803
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.215, 41.514, 72.346
Angle α, β, γ (deg.)90.00, 104.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein carbonic anhydrase II / Carbonic anhydrase / E.C.4.2.1.1 / Carbonic anhydrase 2 / Carbonate dehydratase II / CA-II / Carbonic anhydrase C / CAC


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.3 M Ammonium citrate, 100 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 91517 / % possible obs: 93.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Χ2: 1.753
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.1-1.125.80.50644101.377189.7
1.12-1.1460.42243881.452189.9
1.14-1.166.20.39544101.452190.6
1.16-1.186.40.36144671.541191
1.18-1.216.60.3544621.484191.2
1.21-1.246.70.33944781.506191.7
1.24-1.2770.33244891.52192
1.27-1.37.20.30545431.615192.7
1.3-1.347.30.28745681.626192.7
1.34-1.397.40.26545341.546193.3
1.39-1.447.40.21746061.648193.7
1.44-1.497.40.16846131.509194.2
1.49-1.567.40.13646531.573194.6
1.56-1.647.40.10746771.538195
1.64-1.757.30.09246861.667195.5
1.75-1.887.30.07447331.935196.1
1.88-2.077.40.05447821.695196.7
2.07-2.377.50.04548021.817197.4
2.37-2.987.50.04348912.217198
2.98-206.30.05543254.55185.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CBA
Resolution: 1.1→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.139 4575 -RANDOM
Rwork0.104 ---
all0.1041 91517 --
obs0.1041 91517 92.7 %-
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 15.715 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 12 352 2413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d2.1
LS refinement shellResolution: 1.1→1.12 Å / % reflection obs: 89.7 %

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