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- PDB-9gaj: X-ray structure of HCA(II)/aromatic foldamer complex -

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Basic information

Entry
Database: PDB / ID: 9gaj
TitleX-ray structure of HCA(II)/aromatic foldamer complex
Components
  • Aromatic foldamer
  • Carbonic anhydrase 2
KeywordsPROTEIN BINDING / arbonic anhydrase / aromatic oligoamide foldamer
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, 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: 1.64 Å
AuthorsWang, L. / Langlois d'Estaintot, B. / Fischer, L. / Huc, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of HCA(II)/aromatic foldamer complex
Authors: Wang, L. / Langlois d'Estaintot, B. / Fischer, L. / Huc, I.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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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)32,6024
Polymers32,4442
Non-polymers1582
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, Homology of the HCA2/foldamer complex with 6Q9T, surface plasmon resonance, Nanomolar affinity has been measured for this complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.512, 81.515, 45.893
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: 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00918, carbonic anhydrase
#2: Protein/peptide Aromatic foldamer


Mass: 3155.203 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: 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.53 Å3/Da / Density % sol: 51.45 % / Description: Platelet
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: lithium sulfate, TRIS, PEG 4000, sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2020
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.64→45.893 Å / Num. obs: 67930 / % possible obs: 97 % / Redundancy: 2.43 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.056 / Rrim(I) all: 0.092 / Net I/σ(I): 7.34
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.64-1.742.310.51107920.229195.7
1.74-1.862.451.02103540.48197.3
1.86-22.532.1297950.789198.8
2-2.22.493.8290210.923198.7
2.2-2.452.326.0280010.966197.2
2.45-2.832.4710.3270930.986197.5
2.83-3.472.518.759090.996196.3
3.47-4.892.3226.344540.997193.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→40.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.261 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21085 1131 3.1 %RANDOM
Rwork0.18359 ---
obs0.18448 35448 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å20 Å2
2---2.05 Å2-0 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.64→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 7 278 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162128
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.7853240
X-RAY DIFFRACTIONr_angle_other_deg0.3931.864896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1195262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.87457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46410353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023260
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02577
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_it2.0082.0731057
X-RAY DIFFRACTIONr_mcbond_other2.0052.0721056
X-RAY DIFFRACTIONr_mcangle_it3.0993.691302
X-RAY DIFFRACTIONr_mcangle_other3.13.6891299
X-RAY DIFFRACTIONr_scbond_it2.7562.4871332
X-RAY DIFFRACTIONr_scbond_other2.7552.491333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3454.3851937
X-RAY DIFFRACTIONr_long_range_B_refined7.25726.852791
X-RAY DIFFRACTIONr_long_range_B_other7.25626.862792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.68 Å
RfactorNum. reflection% reflection
Rfree0.385 78 -
Rwork0.412 2455 -
obs--95.77 %
Refinement TLS params.Method: refined / Origin x: 21.1514 Å / Origin y: 12.4762 Å / Origin z: 11.3609 Å
111213212223313233
T0.1511 Å20.0141 Å20.0059 Å2-0.1268 Å20.0004 Å2--0.0033 Å2
L0.7612 °2-0.3227 °2-0.3125 °2-1.588 °20.4667 °2--0.7546 °2
S0.0842 Å °0.049 Å °0.0399 Å °-0.2787 Å °-0.0406 Å °-0.0297 Å °-0.049 Å °-0.0058 Å °-0.0436 Å °

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