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- PDB-5aml: Three dimensional structure of human carbonic anhydrase II in com... -

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Basic information

Entry
Database: PDB / ID: 5aml
TitleThree dimensional structure of human carbonic anhydrase II in complex with 2-(But-2-yn-1-ylsulfamoyl)-4-sulfamoylbenzoic acid
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / CA II / CA 2
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / 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
Chem-51J / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLeitans, J. / Tars, K. / Zalubovskis, R.
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: X-Ray Crystallography-Promoted Drug Design of Carbonic Anhydrase Inhibitors.
Authors: Ivanova, J. / Leitans, J. / Tanc, M. / Kazaks, A. / Zalubovskis, R. / Supuran, C.T. / Tars, K.
History
DepositionMar 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5563
Polymers29,1581
Non-polymers3982
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.280, 41.620, 72.040
Angle α, β, γ (deg.)90.00, 104.48, 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 / CARBON IC ANHYDRASE II / CA-II / CARBONIC ANHYDRASE II


Mass: 29157.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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-51J / 2-(BUT-2-YN-1-YLSULFAMOYL)-4-SULFAMOYLBENZOIC ACID


Mass: 332.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O6S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 42 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, ...Details: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-5 DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.99999
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2013 / Details: MULTILAYER
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.36→20 Å / Num. obs: 52730 / % possible obs: 99.8 % / Observed criterion σ(I): 2.4 / Redundancy: 2.6 % / Biso Wilson estimate: 8.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10
Reflection shellResolution: 1.36→1.43 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BF1

4bf1


Resolution: 1.36→69.75 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.917 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16114 2685 5.1 %RANDOM
Rwork0.11795 ---
obs0.12016 50028 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.963 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.03 Å2
2--0.05 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.36→69.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 22 347 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192164
X-RAY DIFFRACTIONr_bond_other_d0.0030.022015
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9562951
X-RAY DIFFRACTIONr_angle_other_deg1.00334673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03224.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88715357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.669157
X-RAY DIFFRACTIONr_chiral_restr0.1880.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212449
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02500
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_it1.71.1541042
X-RAY DIFFRACTIONr_mcbond_other1.6871.1511041
X-RAY DIFFRACTIONr_mcangle_it2.1591.7451303
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1571.4331122
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.35234179
X-RAY DIFFRACTIONr_sphericity_free40.253575
X-RAY DIFFRACTIONr_sphericity_bonded12.1554384
LS refinement shellResolution: 1.356→1.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 177 -
Rwork0.239 3702 -
obs--99.33 %

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