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

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Basic information

Entry
Database: PDB / ID: 9gak
TitleX-ray structure of HCA(II)/aromatic foldamer complex
Components
  • Aromatic foldamer
  • Carbonic anhydrase 2
KeywordsPROTEIN BINDING / carbonic 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 / 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 / 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: 2.11 Å
AuthorsReddy, S.P. / Langlois d'Estaintot, B. / Fischer, L. / Huc, I.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission751019European Union
CitationJournal: To Be Published
Title: X-ray structure of HCA(II)/aromatic foldamer complex
Authors: Reddy, S.P. / Langlois d'Estaintot, B. / Fischer, L. / Huc, I.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8156
Polymers32,4732
Non-polymers3424
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, Homology of the HCAII/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)80.250, 81.290, 46.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

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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: 3184.201 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.57 Å3/Da / Density % sol: 52.19 % / Description: bladed crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.2M Lithium sulfate, 0.1M TRIS pH 8.8, 18% PEG 4000, 3mM sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979995 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2019
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979995 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 17876 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.117 / Net I/σ(I): 10.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.11-2.246.571.2227560.5571.45997.1
2.24-2.396.781.8326820.6771.052100
2.39-2.586.522.8625040.8350.648100
2.58-2.836.775.0123060.9470.39100
2.83-3.166.579.6421080.9860.198100
3.16-3.656.5718.618770.9970.199.9
3.65-4.465.9725.8716080.9770.07199.9
4.46-6.286.0432.0512680.9970.05799.7
6.28-506.0337.0946100.9990.03799.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→46.12 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.756 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25244 894 5 %RANDOM
Rwork0.20033 ---
obs0.20302 16979 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.084 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0 Å20 Å2
2---2.29 Å2-0 Å2
3---3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.11→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 254 102 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122397
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162127
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.7813270
X-RAY DIFFRACTIONr_angle_other_deg0.4211.8614907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1985262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.27857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36110350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0510.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023399
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02583
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_it3.1874.4181064
X-RAY DIFFRACTIONr_mcbond_other3.1814.4191061
X-RAY DIFFRACTIONr_mcangle_it4.6187.9361312
X-RAY DIFFRACTIONr_mcangle_other4.6257.9491292
X-RAY DIFFRACTIONr_scbond_it3.3774.6681333
X-RAY DIFFRACTIONr_scbond_other3.3764.671334
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3158.3851954
X-RAY DIFFRACTIONr_long_range_B_refined7.29743.332621
X-RAY DIFFRACTIONr_long_range_B_other7.29643.322613
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 61 -
Rwork0.366 1152 -
obs--93.74 %
Refinement TLS params.Method: refined / Origin x: 21.6368 Å / Origin y: 13.7102 Å / Origin z: 11.4654 Å
111213212223313233
T0.1175 Å2-0.0025 Å2-0.0018 Å2-0.0649 Å2-0.0029 Å2--0.0009 Å2
L0.5217 °20.1653 °20.0822 °2-0.6633 °20.0781 °2--0.4029 °2
S-0.0242 Å °0.0788 Å °-0.0183 Å °-0.027 Å °0.024 Å °-0.0145 Å °0.0055 Å °0.0449 Å °0.0002 Å °

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