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- PDB-6q9t: Protein-aromatic foldamer complex crystal structure -

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Basic information

Entry
Database: PDB / ID: 6q9t
TitleProtein-aromatic foldamer complex crystal structure
Components
  • Aromatic foldamer
  • Carbonic anhydrase 2
KeywordsLYASE / Protein-Foldamer Complex / Protein-Foldamer interactions / Modified Inhibitor / Anchored Foldamer / Quinoline Oligoamide Foldamer / Benzene Sulfonamide modified inhibitor / Lyase-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 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsPost, S. / Langlois d'Estaintot, B. / Fischer, L. / Granier, T. / Huc, I.
CitationJournal: Chemistry / Year: 2019
Title: Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas.
Authors: Reddy, P.S. / Langlois d'Estaintot, B. / Granier, T. / Mackereth, C.D. / Fischer, L. / Huc, I.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Aug 14, 2024Group: Atomic model / Data collection ...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_assembly_prop / pdbx_struct_conn_angle / 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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.gene_src_common_name / _pdbx_database_status.pdb_format_compatible / _pdbx_refine_tls_group.end_auth_seq_id / _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.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
Revision 3.1Oct 23, 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: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2673
Polymers32,2022
Non-polymers651
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.300, 80.960, 45.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 29157.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase
#2: Protein/peptide Aromatic foldamer


Mass: 3044.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.52 Å3/Da / Density % sol: 51 % / Description: parallelogram
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: Ammonium sulfate 0.2 M, Sodium acetate 0.1 M pH 5.7, PEG 4000 14%, Sodium azide 3 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 16, 2018
Details: CRYOGENICALLY COOLED CHANNEL CUT CRYSTAL MONOCHROMATOR, CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 2.68→45.62 Å / Num. obs: 8622 / % possible obs: 98.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 72.25 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.099 / Net I/σ(I): 17.96
Reflection shellResolution: 2.68→2.84 Å / Redundancy: 12.64 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1262 / CC1/2: 0.859 / Rrim(I) all: 0.99 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSVERSION Nov 11, 2017 BUILT=20171111data reduction
XDSVERSION Nov 11, 2017 BUILT=20171111data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 2.68→45.62 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 46.885 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R: 2.129 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26025 431 5 %RANDOM
Rwork0.2148 ---
obs0.21732 8189 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.834 Å2
Baniso -1Baniso -2Baniso -3
1--4.59 Å2-0 Å2-0 Å2
2---7.11 Å20 Å2
3---11.7 Å2
Refinement stepCycle: 1 / Resolution: 2.68→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 225 6 2009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0142080
X-RAY DIFFRACTIONr_bond_other_d0.0080.0181721
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.7842858
X-RAY DIFFRACTIONr_angle_other_deg1.5511.6973953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2925235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40923.17182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.24515253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.909156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022447
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02456
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_it2.6315.164971
X-RAY DIFFRACTIONr_mcbond_other2.6535.207945
X-RAY DIFFRACTIONr_mcangle_it4.4217.7741192
X-RAY DIFFRACTIONr_mcangle_other4.4347.8041180
X-RAY DIFFRACTIONr_scbond_it2.2934.8991105
X-RAY DIFFRACTIONr_scbond_other2.2924.8981106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7567.2821666
X-RAY DIFFRACTIONr_long_range_B_refined6.08754.6292546
X-RAY DIFFRACTIONr_long_range_B_other6.08654.6182547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.676→2.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.725 25 -
Rwork0.545 485 -
obs--80.44 %
Refinement TLS params.Method: refined / Origin x: 21.647 Å / Origin y: 93.752 Å / Origin z: -32.153 Å
111213212223313233
T0.4049 Å20.0067 Å20.0054 Å2-0.2932 Å20.0029 Å2--0.0118 Å2
L2.2127 °2-0.398 °20.2305 °2-3.9027 °2-0.5609 °2--0.1756 °2
S0.0956 Å °0.1791 Å °-0.0058 Å °-0.3389 Å °-0.0765 Å °-0.0737 Å °0.0481 Å °-0.033 Å °-0.0192 Å °

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