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- PDB-5dsk: Structure of CO2 released holo-form of human carbonic anhydrase I... -

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Basic information

Entry
Database: PDB / ID: 5dsk
TitleStructure of CO2 released holo-form of human carbonic anhydrase II with 3 min warming
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase II / CO2 release / Intermediate states
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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKim, C.U. / Park, S.Y. / McKenna, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals
Authors: Kim, C.U. / Song, H. / Avvaru, B.S. / Gruner, S.M. / Park, S. / McKenna, R.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)29,4473
Polymers29,2891
Non-polymers1582
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-36 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.192, 41.304, 72.094
Angle α, β, γ (deg.)90.00, 104.17, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 M sodium citrate 100 mM TrisHCl pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 59456 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rsym value: 0.078 / Net I/σ(I): 26.3
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.544 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D92

3d92


Resolution: 1.3→28.67 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.239 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14422 2988 5 %RANDOM
Rwork0.11039 ---
obs0.11215 56211 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.096 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.03 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 7 399 2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192171
X-RAY DIFFRACTIONr_bond_other_d0.0020.022037
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9512959
X-RAY DIFFRACTIONr_angle_other_deg0.94334728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21924.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3815363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.84157
X-RAY DIFFRACTIONr_chiral_restr0.1410.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212473
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02502
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1311.1481053
X-RAY DIFFRACTIONr_mcbond_other1.1221.1451052
X-RAY DIFFRACTIONr_mcangle_it1.3581.7291321
X-RAY DIFFRACTIONr_mcangle_other1.3641.7311322
X-RAY DIFFRACTIONr_scbond_it1.9621.4431118
X-RAY DIFFRACTIONr_scbond_other1.9621.4441118
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2152.0411633
X-RAY DIFFRACTIONr_long_range_B_refined6.06614.022945
X-RAY DIFFRACTIONr_long_range_B_other4.7211.9562704
X-RAY DIFFRACTIONr_rigid_bond_restr6.80134208
X-RAY DIFFRACTIONr_sphericity_free43.917574
X-RAY DIFFRACTIONr_sphericity_bonded11.4854488
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 207 -
Rwork0.171 4084 -
obs--97.9 %

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