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- PDB-5eoi: Crystal structure of copper bound human Carbonic anhydrase II -

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Basic information

Entry
Database: PDB / ID: 5eoi
TitleCrystal structure of copper bound human Carbonic anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsLYASE
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 / positive regulation of synaptic transmission, GABAergic ...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 / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / 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
COPPER (II) ION / : / OXYGEN MOLECULE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFerraroni, M. / Scozzafava, A. / Supuran, C.T.
CitationJournal: to be published
Title: Crystal structure of copper bound human Carbonic anhydrase II
Authors: Ferraroni, M. / Scozzafava, A. / Supuran, C.T. / Rizzarelli, E. / Tabbi, G.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)29,4686
Polymers29,0711
Non-polymers3975
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-87 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.026, 41.479, 72.067
Angle α, β, γ (deg.)90.000, 104.610, 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: 29070.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: erythrocytes / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 349 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.4 M ammonium sulphate, Tris 50 mM, HgCl2 2mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.542 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Nov 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→14.75 Å / Num. obs: 21538 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 21.093 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.084 / Χ2: 0.909 / Net I/σ(I): 17.12 / Num. measured all: 123479
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.912.40.6950.4781.926744352427710.6178.6
1.91-2.040.9110.3234.2413963333832820.36998.3
2.04-2.20.9680.1978.0216434310331010.21999.9
2.2-2.410.9880.14312.0218672287228720.155100
2.41-2.680.9940.1116.218745262626230.11899.9
2.68-3.080.9980.06824.0616654232123210.073100
3.08-3.730.9990.04237.414323199119900.04699.9
3.73-5.110.9990.03446.1711217157815770.03699.9
5.110.9990.03944.486727105210010.04295.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FIK

4fik


Resolution: 1.8→14.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.1844 / WRfactor Rwork: 0.1263 / FOM work R set: 0.8467 / SU B: 3.116 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1317 / SU Rfree: 0.1329 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 1064 4.9 %RANDOM
Rwork0.1471 ---
obs0.15 20464 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.89 Å2 / Biso mean: 18.379 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.3 Å2
2---0.08 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.8→14.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 6 344 2398
Biso mean--19.48 30.41 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192190
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9442992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78924.757103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34715364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.369157
X-RAY DIFFRACTIONr_chiral_restr0.1440.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211703
X-RAY DIFFRACTIONr_mcbond_it1.7691.5341059
X-RAY DIFFRACTIONr_mcangle_it2.8212.2911328
X-RAY DIFFRACTIONr_scbond_it2.4471.7061131
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 55 -
Rwork0.31 1063 -
all-1118 -
obs--69.57 %

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