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

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Basic information

Entry
Database: PDB / ID: 9gam
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 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 / 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: 1.4 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 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)32,8037
Polymers32,3692
Non-polymers4345
Water6,143341
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)79.596, 81.601, 46.720
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: 3080.052 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.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.59 Å3/Da / Density % sol: 52.51 % / Description: platelet
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M lithium sulfate, 0.1 M TRIS pH 8.5, PEG 4000 20%, 3 mM 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: 0.979999 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: 0.979999 Å / Relative weight: 1
ReflectionResolution: 1.4→65 Å / Num. obs: 60722 / % possible obs: 99.9 % / Redundancy: 13.27 % / CC1/2: 1 / Rrim(I) all: 0.073 / Net I/σ(I): 18.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.4-1.4813.191.1796480.5882.30299.6
1.48-1.5912.922.3591220.8431.188100
1.59-1.7113.514.6785350.9630.611100
1.71-1.8813.348.2878560.9860.332100
1.88-2.113.916.1771380.9960.171100
2.1-2.4213.4126.9963290.9980.098100
2.42-2.9712.9740.5153780.9990.062100
2.97-4.1912.8465.69424710.035100
4.19-6512.9277.44246710.02899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.72 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.117 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 3037 5 %RANDOM
Rwork0.15553 ---
obs0.15689 57685 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.393 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å2-0 Å2
2---0.79 Å2-0 Å2
3---1.84 Å2
Refinement stepCycle: 1 / Resolution: 1.4→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 252 341 2634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122397
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162135
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.7853271
X-RAY DIFFRACTIONr_angle_other_deg0.5481.8534929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9245264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.02557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28410354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023376
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02580
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_it1.6741.9151066
X-RAY DIFFRACTIONr_mcbond_other1.6731.9161063
X-RAY DIFFRACTIONr_mcangle_it2.2583.441315
X-RAY DIFFRACTIONr_mcangle_other2.2623.4451295
X-RAY DIFFRACTIONr_scbond_it3.4762.2261331
X-RAY DIFFRACTIONr_scbond_other3.4782.2271332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1733.8931951
X-RAY DIFFRACTIONr_long_range_B_refined6.46622.292697
X-RAY DIFFRACTIONr_long_range_B_other6.33721.032600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å
RfactorNum. reflection% reflection
Rfree0.395 219 -
Rwork0.391 4150 -
obs--99.21 %
Refinement TLS params.Method: refined / Origin x: 21.5638 Å / Origin y: 14.4621 Å / Origin z: 11.6472 Å
111213212223313233
T0.0272 Å20.0032 Å2-0.0153 Å2-0.0105 Å2-0.0006 Å2--0.0207 Å2
L0.6784 °2-0.1386 °2-0.0966 °2-0.4715 °20.2247 °2--0.1981 °2
S0.0465 Å °0.0286 Å °0.0552 Å °-0.0158 Å °-0.001 Å °-0.0237 Å °0.0327 Å °-0.0111 Å °-0.0455 Å °

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