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- PDB-5l3o: Crystal Structure of Human Carbonic Anhydrase II in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 5l3o
TitleCrystal Structure of Human Carbonic Anhydrase II in Complex with a Quinoline Oligoamide Foldamer
ComponentsCarbonic anhydrase 2
KeywordsLyase/Inhibitor / PROTEIN-FOLDAMER COMPLEX / PROTEIN FOLDAMER INTERACTIONS / MODIFIED INHIBITOR / ANCHORED FOLDAMER / HCAII DIMERISATION / QUINOLINE OLIGOAMIDE FOLDAMER / BENZENE SULFONAMIDE MODIFIED INHIBITOR / 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 / molecular replacement / Resolution: 1.98 Å
AuthorsJewginski, M. / Langlois d'Estaintot, B. / Granier, T. / Huc, Y.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish Ministry of Science and 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 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_auth_seq_id / _audit_author.name / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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)64,92731
Polymers58,5782
Non-polymers6,34929
Water4,684260
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,41815
Polymers29,2891
Non-polymers3,12914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,51016
Polymers29,2891
Non-polymers3,22115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.880, 54.480, 84.920
Angle α, β, γ (deg.)90.000, 112.790, 90.000
Int Tables number5
Space group name H-MC121
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 8 types, 289 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 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 405.468 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C19H23N3O5S / Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: carbonic anhydrase
#4: Chemical
ChemComp-QUK / 8-azanyl-4-(3-azanylpropoxy)quinoline-2-carboxylic acid / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 261.276 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C13H15N3O3 / Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: carbonic anhydrase
#5: Chemical
ChemComp-QVS / 8-azanyl-4-oxidanyl-quinoline-2-carboxylic acid / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 204.182 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H8N2O3 / Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: carbonic anhydrase
#6: Chemical
ChemComp-QVE / 8-azanyl-4-(2-hydroxy-2-oxoethyloxy)quinoline-2-carboxylic acid / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 262.218 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C12H10N2O5 / Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: carbonic anhydrase
#7: Chemical
ChemComp-GOL / GLYCEROL / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C3H8O3 / Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: carbonic anhydrase
#8: Chemical
ChemComp-QUJ / 8-azanyl-4-(2-methylpropoxy)quinoline-2-carboxylic acid / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 260.288 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H16N2O3 / Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: carbonic anhydrase
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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, sitting drop / pH: 4.6 / Details: NA acetate, PEG 4000, NaN3

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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: Mar 13, 2015 / Details: Pt coated Si 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: 1.98→78.29 Å / Num. obs: 46107 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 34.12 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.9
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.9 / % possible all: 92.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.585
Highest resolutionLowest resolution
Rotation45.63 Å2.03 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.98→78.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 2271 4.9 %RANDOM
Rwork0.2066 ---
obs0.2081 43836 98.27 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 102.8 Å2 / Biso mean: 43.816 Å2 / Biso min: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å21.99 Å2
2---0.87 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.98→78.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 370 260 4754
Biso mean--42.11 45.79 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194655
X-RAY DIFFRACTIONr_bond_other_d00.024190
X-RAY DIFFRACTIONr_angle_refined_deg1.6592.0256337
X-RAY DIFFRACTIONr_angle_other_deg3.6263.0089657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7355520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65924.747198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86715706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0721513
X-RAY DIFFRACTIONr_chiral_restr0.090.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215257
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021092
X-RAY DIFFRACTIONr_mcbond_it2.3492.4792102
X-RAY DIFFRACTIONr_mcbond_other2.3422.4682087
X-RAY DIFFRACTIONr_mcangle_it3.1393.6862602
Refine LS restraints NCS

Ens-ID: 1 / Number: 31998 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 159 -
Rwork0.33 2730 -
all-2889 -
obs--83.84 %
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)
12.22180.1741-0.09561.6197-0.52033.0622-0.06360.0308-0.1037-0.0723-0.01660.01570.18520.06060.08030.0958-0.04270.05830.1063-0.03160.0402-53.387-15.359-18.839
21.99650.47940.06221.80470.06822.0117-0.0587-0.0045-0.2123-0.07810.0748-0.09590.0516-0.0218-0.0160.0799-0.03490.04610.18260.02070.0526-14.29-0.002-23.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 260
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B2 - 260
4X-RAY DIFFRACTION2B305

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