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- PDB-6q3o: PROTEIN-AROMATIC FOLDAMER COMPLEX CRYSTAL STRUCTURE -

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Entry
Database: PDB / ID: 6q3o
TitlePROTEIN-AROMATIC FOLDAMER COMPLEX CRYSTAL STRUCTURE
Components
  • Aromatic foldamer
  • Carbonic anhydrase 2
KeywordsLYASE / PROTEIN-FOLDAMER COMPLEX QUINOLINE OPROTEIN-FOLDAMER INTERACTIONSLIGOAMIDE FOLDAMER BENZENE SULFONAMIDE MODIFIED INHIBITOR
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 / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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, 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
4-sulfamoylbenzoic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsZeberko, C. / Langlois d'Estaintot, B. / Fischer, L. / Granier, T. / Kauffmann, B. / Huc, I.
CitationJournal: To Be Published
Title: PROTEIN-AROMATIC FOLDAMER COMPLEX CRYSTAL STRUCTURE
Authors: Zeberko, C.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 2.1Jan 24, 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 / Refinement description / 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_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_peptide_omega / 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 / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.pdb_format_compatible / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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
Revision 3.1Oct 16, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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
D: Carbonic anhydrase 2
H: Aromatic foldamer
E: Aromatic foldamer
F: Aromatic foldamer
G: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,29842
Polymers121,5058
Non-polymers2,79434
Water12,502694
1
A: Carbonic anhydrase 2
C: Carbonic anhydrase 2
H: Aromatic foldamer
F: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,22822
Polymers60,7524
Non-polymers1,47618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 2
D: Carbonic anhydrase 2
E: Aromatic foldamer
G: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,07020
Polymers60,7524
Non-polymers1,31816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.106, 76.478, 81.417
Angle α, β, γ (deg.)66.10, 86.83, 73.60
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / 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: 4 - 260 / Label seq-ID: 3 - 259

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDHEFG

#1: Protein
Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29157.863 Da / Num. of mol.: 4
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) / References: UniProt: P00918, carbonic anhydrase
#2: Protein/peptide
Aromatic foldamer


Mass: 1218.275 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 728 molecules

#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Zn
#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: Chemical
ChemComp-4SO / 4-sulfamoylbenzoic acid


Mass: 201.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7NO4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.46 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Zn acetate 0.2 M, Na cacodylate 0.1 M, PEG 8000 18%, NaN3 3mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 9, 2018 / Details: Mirrors Osmic Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.23→28.29 Å / Num. obs: 60589 / % possible obs: 99.2 % / Redundancy: 1.89 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.88
Reflection shellResolution: 2.23→2.33 Å / Redundancy: 1.76 % / Num. unique obs: 7450 / Rsym value: 0.398 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KS3

2ks3
PDB Unreleased entry


Resolution: 2.23→28.29 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.587 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25291 2994 4.9 %RANDOM
Rwork0.21196 ---
obs0.21397 57539 99.53 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 31.611 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.12 Å20.82 Å2
2--0.03 Å2-0.12 Å2
3----0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.23→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8124 0 447 694 9265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0138895
X-RAY DIFFRACTIONr_bond_other_d0.0180.0187830
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.71112087
X-RAY DIFFRACTIONr_angle_other_deg1.8071.63418199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81851028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47423.534416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.234151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6561529
X-RAY DIFFRACTIONr_chiral_restr0.0770.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.029918
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021861
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_it0.9831.5994136
X-RAY DIFFRACTIONr_mcbond_other0.9821.5984129
X-RAY DIFFRACTIONr_mcangle_it1.3282.3935142
X-RAY DIFFRACTIONr_mcangle_other1.3292.3925140
X-RAY DIFFRACTIONr_scbond_it1.0191.6974759
X-RAY DIFFRACTIONr_scbond_other1.0191.6974760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3682.5136944
X-RAY DIFFRACTIONr_long_range_B_refined1.82118.45610394
X-RAY DIFFRACTIONr_long_range_B_other1.8218.30410243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85020.06
12B85020.06
21A84770.07
22C84770.07
31A85310.06
32D85310.06
41B85750.05
42C85750.05
51B84890.06
52D84890.06
61C85270.06
62D85270.06
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 229 -
Rwork0.317 4235 -
obs--99 %
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)
11.1419-0.1020.05562.04620.20121.2346-0.0002-0.03040.03660.15280.01540.0564-0.0542-0.0616-0.01510.1968-0.0201-0.11660.01080.01040.0992-0.051-0.241-0.002
21.68890.64140.1331.8242-0.0421.347-0.09560.06440.0523-0.09750.04870.13810.0385-0.0370.04690.1921-0.0457-0.13270.02130.0090.1511-13.247-43.759-22.007
31.3262-0.17650.29871.99930.21562.1344-0.0121-0.1967-0.05780.40340.0934-0.11490.22820.0397-0.08130.32290.0138-0.1610.0368-0.00040.115618.933-31.0514.207
41.2953-0.1893-0.38641.61640.65042.91740.03980.03950.1268-0.34330.1861-0.1355-0.36870.2606-0.22590.2898-0.1286-0.05670.0974-0.02840.135416.139-22.702-35.475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 260
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A306
4X-RAY DIFFRACTION1E4
5X-RAY DIFFRACTION1A309
6X-RAY DIFFRACTION1A303
7X-RAY DIFFRACTION1A310
8X-RAY DIFFRACTION1A302
9X-RAY DIFFRACTION1A304
10X-RAY DIFFRACTION2B4 - 260
11X-RAY DIFFRACTION2B301
12X-RAY DIFFRACTION2E5
13X-RAY DIFFRACTION2B303
14X-RAY DIFFRACTION2A308
15X-RAY DIFFRACTION2B302
16X-RAY DIFFRACTION2B304
17X-RAY DIFFRACTION2B305
18X-RAY DIFFRACTION2B306
19X-RAY DIFFRACTION3C4 - 260
20X-RAY DIFFRACTION3C301
21X-RAY DIFFRACTION3C305
22X-RAY DIFFRACTION3C302
23X-RAY DIFFRACTION3C303
24X-RAY DIFFRACTION4D4 - 260
25X-RAY DIFFRACTION4D301
26X-RAY DIFFRACTION4D304
27X-RAY DIFFRACTION4E3
28X-RAY DIFFRACTION4D306
29X-RAY DIFFRACTION4D302
30X-RAY DIFFRACTION4D303

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