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- PDB-4mty: Structure at 1A resolution of a helical aromatic foldamer-protein... -

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Basic information

Entry
Database: PDB / ID: 4mty
TitleStructure at 1A resolution of a helical aromatic foldamer-protein complex.
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Mixed Alpha Beta / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 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
: / 4-(HYDROXYMERCURY)BENZOIC ACID / N-(3-hydroxybenzyl)-4-sulfamoylbenzamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsOgayone, T. / Buratto, J. / Langlois D'Estaintot, B. / Stupfel, M. / Granier, T. / Gallois, B. / Huc, Y.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Structure of a complex formed by a protein and a helical aromatic oligoamide foldamer at 2.1 a resolution.
Authors: Buratto, J. / Colombo, C. / Stupfel, M. / Dawson, S.J. / Dolain, C. / Langlois d'Estaintot, B. / Fischer, L. / Granier, T. / Laguerre, M. / Gallois, B. / Huc, I.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Jul 5, 2017Group: Refinement description / Structure summary / Category: software / struct / Item: _struct.title
Revision 1.3Jul 19, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_ptnr1_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_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)31,18111
Polymers29,2891
Non-polymers1,89210
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.444, 41.559, 72.064
Angle α, β, γ (deg.)90.000, 104.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29289.062 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 (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 408 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SBW / N-(3-hydroxybenzyl)-4-sulfamoylbenzamide


Mass: 306.337 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H14N2O4S
#4: Chemical ChemComp-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6HgO3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.15 mM HCA2, 50 mM TRIS pH 8.5, 150 mM NaCl, 2mM 4-(hydroxymercury)benzoate, 2.7 M (NH4)2SO4, 3 mM NaN3, 0.75 mM benzamide N-(3-hydroxybenzyl)-4-sulfamoyl., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2008 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1→29.22 Å / Num. all: 128713 / Num. obs: 128713 / % possible obs: 98.18 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11.147
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allDiffraction-ID% possible all
1-1.053.50.226627018916199.24
1.05-1.123.510.166299617934199.2
1.12-1.23.530.135944316858199.41
1.2-1.293.530.125523815663199.09
1.29-1.413.530.115112314475199.16
1.41-1.583.490.14546013016198.96
1.58-1.833.30.093802311506198.93
1.83-2.243.550.09348989830199.2
2.24-3.163.540.09267307548198.44
3.16-29.222.840.0984312967169.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALACCP4_3.2.21data scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CA2

1ca2


Resolution: 1→28.85 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1261 / WRfactor Rwork: 0.1056 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9609 / SU B: 0.408 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0174 / SU Rfree: 0.0184 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.017 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1226 6479 5 %RANDOM
Rwork0.1047 ---
all0.1056 128692 --
obs0.1056 128692 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.62 Å2 / Biso mean: 12.1161 Å2 / Biso min: 3.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20.05 Å2
2--0.05 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 99 398 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192294
X-RAY DIFFRACTIONr_bond_other_d0.0020.022059
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9863141
X-RAY DIFFRACTIONr_angle_other_deg1.49934765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9425289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52524.653101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.4615345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.054158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212654
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02543
X-RAY DIFFRACTIONr_mcbond_it1.2091093
X-RAY DIFFRACTIONr_mcbond_other1.2031092
X-RAY DIFFRACTIONr_mcangle_it1.5681385
X-RAY DIFFRACTIONr_rigid_bond_restr7.42632189
X-RAY DIFFRACTIONr_sphericity_free28.896557
X-RAY DIFFRACTIONr_sphericity_bonded9.7152380
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 446 -
Rwork0.162 9121 -
all-9567 -
obs--99.03 %

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