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- PDB-2w3n: Structure and inhibition of the CO2-sensing carbonic anhydrase Ca... -

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Basic information

Entry
Database: PDB / ID: 2w3n
TitleStructure and inhibition of the CO2-sensing carbonic anhydrase Can2 from the pathogenic fungus Cryptococcus neoformans
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / BETA-CLASS CARBONIC ANHYDRASE / INHIBITION / SULFONAMIDE / CRYPTOCOCCUS NEOFORMANS
Function / homology
Function and homology information


cellular response to carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / zinc ion binding
Similarity search - Function
Helix Hairpins - #610 / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / Helix Hairpins / Helix non-globular / Special ...Helix Hairpins - #610 / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / Helix Hairpins / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Carbonic anhydrase
Similarity search - Component
Biological speciesCRYPTOCOCCUS NEOFORMANS (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchlicker, C. / Hall, R.A. / Vullo, D. / Middelhaufe, S. / Gertz, M. / Supuran, C.T. / Muehlschlegel, F.A. / Steegborn, C.
CitationJournal: J. Mol. Biol. / Year: 2009
Title: Structure and inhibition of the CO2-sensing carbonic anhydrase Can2 from the pathogenic fungus Cryptococcus neoformans.
Authors: Schlicker, C. / Hall, R.A. / Vullo, D. / Middelhaufe, S. / Gertz, M. / Supuran, C.T. / Muhlschlegel, F.A. / Steegborn, C.
History
DepositionNov 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / diffrn_radiation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE 2
B: CARBONIC ANHYDRASE 2
C: CARBONIC ANHYDRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,35910
Polymers79,8943
Non-polymers4657
Water2,594144
1
B: CARBONIC ANHYDRASE 2
C: CARBONIC ANHYDRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5116
Polymers53,2622
Non-polymers2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-57.6 kcal/mol
Surface area22540 Å2
MethodPQS
2
A: CARBONIC ANHYDRASE 2
hetero molecules

A: CARBONIC ANHYDRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6958
Polymers53,2622
Non-polymers4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7710 Å2
ΔGint-46.2 kcal/mol
Surface area24260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)177.980, 56.590, 83.220
Angle α, β, γ (deg.)90.00, 116.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21A-2025-

HOH

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Components

#1: Protein CARBONIC ANHYDRASE 2 / CARBONIC ANHYDRASE


Mass: 26631.186 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRYPTOCOCCUS NEOFORMANS (Cryptococcus neoformans serotype A)
Variant: GRUBII / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q3I4V7, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.35 Å3/Da / Density % sol: 47.66 % / Description: NONE
Crystal growDetails: 24% PEG3350, 0.2 M AMMONIUM ACETATE, 0.01 M MAGNESIUM ACETATE, 0.05M SODIUM CACODYLATE PH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.05→46.8 Å / Num. obs: 46398 / % possible obs: 98.5 % / Observed criterion σ(I): 3.01 / Redundancy: 1 % / Rmerge(I) obs: 0.13
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 1 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 3.01 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T75

1t75


Resolution: 2.05→79.56 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.487 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23086 2337 5 %RANDOM
Rwork0.18653 ---
obs0.18878 44060 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.694 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-0.38 Å2
2--1.36 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.05→79.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 21 144 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9467344
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1855674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23524.683252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1415864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2171530
X-RAY DIFFRACTIONr_chiral_restr0.1030.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024183
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.22463
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23690
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5211.53462
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34125477
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.83632185
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7834.51867
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 161
Rwork0.235 3271

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