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- PDB-5g03: An unusual natural product primary sulfonamide: synthesis, carbon... -

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Basic information

Entry
Database: PDB / ID: 5g03
TitleAn unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition and protein x-ray structure of Psammaplin C
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / NATURAL PRODUCT INHIBITOR / PROTEIN ENGINEERING / CARBONIC ANHYDRASE
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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 / cytoplasm / cytosol
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
PSAMMAPLIN C / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMujumdar, P. / Supuran, C.T. / Peat, T.S. / Poulsen, S.A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structures of Psammaplin C.
Authors: Mujumdar, P. / Teruya, K. / Tonissen, K.F. / Vullo, D. / Supuran, C.T. / Peat, T.S. / Poulsen, S.
History
DepositionMar 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jan 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7694
Polymers29,2271
Non-polymers5423
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.880, 41.280, 71.788
Angle α, β, γ (deg.)90.00, 104.11, 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: 29226.859 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 1-260 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CAII PROTEIN MUTATED IN ACTIVE SITE TO MIMIC CAIX PROTEIN
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OE2 / PSAMMAPLIN C


Mass: 380.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14BrN3O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCAII PROTEIN MUTATED TO MIMIC CAIX PROTEIN WITH THE FOLLOWING MUTATIONS A65S, N67Q, E69T, I91L, ...CAII PROTEIN MUTATED TO MIMIC CAIX PROTEIN WITH THE FOLLOWING MUTATIONS A65S, N67Q, E69T, I91L, F131V, G132D, V135L, K170E, L204A, C206G

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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: 41.2 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 150 NL PROTEIN AT 5.5 MG/ML PLUS 120 NL RESERVOIR AND 30 NL SEEDS IN SITTING DROP PLATES. RESERVOIR WAS 2.6 TO 2.8 M AMMONIUM SULFATE PLUS 100 MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.35→41.3 Å / Num. obs: 50188 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.4 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6H

5a6h


Resolution: 1.35→69.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.888 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE INHIBITOR IS MOSTLY DISORDERED BEYOND THE SULFONAMIDE WHICH IS BOUND TO THE ZINC ATOM. THE WHOLE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE INHIBITOR IS MOSTLY DISORDERED BEYOND THE SULFONAMIDE WHICH IS BOUND TO THE ZINC ATOM. THE WHOLE MOLECULE IS MODELLED ALTHOUGH THERE IS LITTLE DENSITY BEYOND THE SECOND CARBON LINKING THE SULFONAMIDE TO THE REST OF THE COMPOUND.
RfactorNum. reflection% reflectionSelection details
Rfree0.16005 2467 4.9 %RANDOM
Rwork0.1275 ---
obs0.12909 47704 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.03 Å2
2--0.18 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.35→69.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 27 261 2333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192303
X-RAY DIFFRACTIONr_bond_other_d0.0030.022136
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.963152
X-RAY DIFFRACTIONr_angle_other_deg1.08634971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5325104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12615386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.113157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212689
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02529
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_it1.3421.2241121
X-RAY DIFFRACTIONr_mcbond_other1.3341.2211120
X-RAY DIFFRACTIONr_mcangle_it1.7041.8451428
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6691.5491182
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_restr4.43834439
X-RAY DIFFRACTIONr_sphericity_free30.807526
X-RAY DIFFRACTIONr_sphericity_bonded9.08454597
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 180 -
Rwork0.223 3335 -
obs--90.94 %

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