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- PDB-5l6k: Crystal Structure of Human Carbonic Anhydrase II in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5l6k
TitleCrystal Structure of Human Carbonic Anhydrase II in Complex with a Quinoline Oligoamide Foldamer
ComponentsCarbonic anhydrase 2
KeywordsLYASE / PROTEIN-FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / MODIFIED INHIBITOR / ANCHORED FOLDAMER / HCAII DIMERISATION / 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 / 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
Chem-6H0 / Chem-QUJ / Chem-QUK / Chem-QVE / 8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJewginski, M. / Langlois d'Estaintot, B. / Granier, T. / Huc, Y.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish Ministry of Science and Higher EducationMobility Plus Program Poland
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Self-Assembled Protein-Aromatic Foldamer Complexes with 2:3 and 2:2:1 Stoichiometries.
Authors: Jewginski, M. / Granier, T. / Langlois d'Estaintot, B. / Fischer, L. / Mackereth, C.D. / Huc, I.
History
DepositionMay 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / pdbx_unobs_or_zero_occ_atoms / struct / struct_conn / struct_site / struct_site_gen
Item: _atom_site.label_alt_id / _audit_author.name / _struct.title
Revision 2.1Aug 21, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_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_asym_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,33030
Polymers58,5782
Non-polymers5,75228
Water7,152397
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,21516
Polymers29,2891
Non-polymers2,92615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,11414
Polymers29,2891
Non-polymers2,82513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.070, 84.870, 77.220
Angle α, β, γ (deg.)90.000, 97.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 2 - 260 / Label seq-ID: 2 - 260

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29289.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: PET11D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 11 types, 425 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6H0 / ~{N}-[[3-(4-formamidobutoxy)phenyl]methyl]-4-sulfamoyl-benzamide


Mass: 405.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N3O5S
#4: Chemical
ChemComp-QUK / 8-azanyl-4-(3-azanylpropoxy)quinoline-2-carboxylic acid


Mass: 261.276 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H15N3O3
#5: Chemical
ChemComp-QVS / 8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid


Mass: 204.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H8N2O3
#6: Chemical
ChemComp-QVE / 8-azanyl-4-(2-hydroxy-2-oxoethyloxy)quinoline-2-carboxylic acid


Mass: 262.218 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C12H10N2O5
#7: 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
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical
ChemComp-QUJ / 8-azanyl-4-(2-methylpropoxy)quinoline-2-carboxylic acid


Mass: 260.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16N2O3
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: NaAc, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 14, 2015 / Details: half-Kirkpatrick-Baez (KB) mirrors
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→78.64 Å / Num. obs: 61725 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.238 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.34
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.760.6931.93199.8
1.76-1.830.5312.5199.5
1.83-1.910.4173.39199.7
1.91-2.010.2954.82199.3
2.01-2.140.2276.8199.7
2.14-2.30.1738.93199.9
2.3-2.520.12710.94199.7
2.52-2.90.08814.98199.9
2.9-3.70.05224.54199.8
3.70.03733.46199.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDS1.3.2015data reduction
SCALA1.3.2015data scaling
PHASER6.5.016phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.7→76.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.792 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1813 3137 5.1 %RANDOM
Rwork0.1536 ---
obs0.155 58588 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 103.18 Å2 / Biso mean: 25.343 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.84 Å2
2--1.22 Å20 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 1.7→76.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 357 397 4868
Biso mean--25.83 36.77 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194697
X-RAY DIFFRACTIONr_bond_other_d0.0010.024250
X-RAY DIFFRACTIONr_angle_refined_deg1.8682.0176413
X-RAY DIFFRACTIONr_angle_other_deg3.6943.0069801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41624.596198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4515718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0141514
X-RAY DIFFRACTIONr_chiral_restr0.1230.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215362
X-RAY DIFFRACTIONr_gen_planes_other0.0260.021120
X-RAY DIFFRACTIONr_mcbond_it2.4241.2622132
X-RAY DIFFRACTIONr_mcbond_other2.3791.2512117
X-RAY DIFFRACTIONr_mcangle_it3.1771.8632648
Refine LS restraints NCS

Ens-ID: 1 / Number: 32064 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 229 -
Rwork0.267 4283 -
all-4512 -
obs--99.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0834-0.04970.11360.9282-0.05481.0954-0.02350.05070.0396-0.03870.0121-0.0037-0.0440.01630.01140.0610.0091-0.03090.0052-0.00210.037720.05822.56547.461
21.1876-0.14990.2330.89990.06721.51220.0633-0.007-0.0659-0.0139-0.0119-0.01430.0172-0.0274-0.05140.0905-0.0017-0.04620.0371-0.00960.048532.26825.38787.624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 260
2X-RAY DIFFRACTION2B2 - 260

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