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- PDB-5l70: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH ... -

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Entry
Database: PDB / ID: 5l70
TitleCRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER
Components
  • Aromatic foldamer
  • Carbonic anhydrase 2
KeywordsLyase/Inhibitor / PROTEIN-FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / MODIFIED INHIBITOR / ANCHORED FOLDAMER / HCAII DIMERISATION / QUINOLINE OLIGOAMIDE FOLDAMER / BENZENE SULFONAMIDE MODIFIED INHIBITOR / LYASE-INHIBITOR COMPLEX
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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVallade, M. / Langlois d'Estaintot, B. / Granier, T. / Huc, I.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH A QUINOLINE OLIGOAMIDE FOLDAMER
Authors: Vallade, M. / Fischer, L. / Langlois d'Estaintot, B. / Granier, T. / Huc, I.
History
DepositionJun 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name / _citation_author.name
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Sep 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_src_gen.gene_src_common_name / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 4.0Oct 2, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 4.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Aromatic foldamer
D: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,53621
Polymers61,3174
Non-polymers1,21917
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.210, 83.370, 79.410
Angle α, β, γ (deg.)90.000, 99.980, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 260 / Label seq-ID: 3 - 260

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pet11d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase
#2: Protein/peptide Aromatic foldamer


Mass: 1369.370 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: ZnOAc, NaCac, PEG 8000, NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2015 / Details: Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.2→83.37 Å / Num. obs: 27767 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rsym value: 0.128 / Net I/av σ(I): 4.182 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.323.20.3481.9196.1
2.32-2.463.20.2872.3196.6
2.46-2.633.30.2213197.4
2.63-2.843.30.1773.6196.9
2.84-3.113.20.1394.6197
3.11-3.483.20.1135.2196.9
3.48-4.023.10.0956.5196.1
4.02-4.923.10.0986191
4.92-6.963.40.0956.1198.5
6.96-43.5413.20.0885.9197.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SCALA3.3.22data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 2.2→78.21 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.133 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.225
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1402 5.1 %RANDOM
Rwork0.1737 ---
obs0.1769 26346 96.02 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.81 Å2 / Biso mean: 31.766 Å2 / Biso min: 8.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.25 Å2
2--1.49 Å20 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 2.2→78.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 235 334 4576
Biso mean--27.57 34.75 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024432
X-RAY DIFFRACTIONr_bond_other_d0.0060.023910
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9856013
X-RAY DIFFRACTIONr_angle_other_deg1.6263.0088946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15224.583192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77115623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9471513
X-RAY DIFFRACTIONr_chiral_restr0.080.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215027
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021037
X-RAY DIFFRACTIONr_mcbond_it3.3071.8242085
X-RAY DIFFRACTIONr_mcbond_other3.2951.822077
X-RAY DIFFRACTIONr_mcangle_it4.4642.7192594
Refine LS restraints NCS

Ens-ID: 1 / Number: 30262 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 103 -
Rwork0.214 1915 -
all-2018 -
obs--95.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3591-0.08820.24110.54140.01820.7819-0.0210.00950.039-0.012-0.01380.01610.051-0.04750.03480.0948-0.00250.00080.0053-0.00660.218540.96612.85632.334
20.40660.03220.48980.40830.66262.5478-0.1134-0.03090.09790.1159-0.11810.0510.2774-0.05580.23140.12770.0110.04320.05720.00130.187153.89821.10568.001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 260
2X-RAY DIFFRACTION1A300
3X-RAY DIFFRACTION2B3 - 260
4X-RAY DIFFRACTION2B300

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