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- PDB-4ywp: Sucrose Binding Site in genetically engineered Carbonic anhydrase IX -

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Basic information

Entry
Database: PDB / ID: 4ywp
TitleSucrose Binding Site in genetically engineered Carbonic anhydrase IX
ComponentsCarbonic anhydrase 2
KeywordsLYASE / alpha-carbonic anhydrase / CA IX mimic / sucrose
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 / morphogenesis of an epithelium / 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 / 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
sucrose / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPinard, M.A. / Aggarwal, M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: A sucrose-binding site provides a lead towards an isoform-specific inhibitor of the cancer-associated enzyme carbonic anhydrase IX.
Authors: Pinard, M.A. / Aggarwal, M. / Mahon, B.P. / Tu, C. / McKenna, R.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2523
Polymers28,8441
Non-polymers4082
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-37 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.845, 41.240, 72.275
Angle α, β, γ (deg.)90.00, 103.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28844.465 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F131V, K170E, L204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris-HCL pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 42193 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rsym value: 0.05 / Net I/av σ(I): 16.3 / Net I/σ(I): 9.744
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 11.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.45→20 Å / SU ML: 0.12 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 2006 4.76 %
Rwork0.162 --
obs0.1633 42138 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 24 285 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092133
X-RAY DIFFRACTIONf_angle_d1.4022902
X-RAY DIFFRACTIONf_dihedral_angle_d13.47784
X-RAY DIFFRACTIONf_chiral_restr0.081312
X-RAY DIFFRACTIONf_plane_restr0.009371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48440.20041400.16742844X-RAY DIFFRACTION97
1.4844-1.52450.21791430.16332872X-RAY DIFFRACTION100
1.5245-1.56930.18581490.15852893X-RAY DIFFRACTION100
1.5693-1.620.1821460.15592880X-RAY DIFFRACTION100
1.62-1.67780.18071430.15882910X-RAY DIFFRACTION100
1.6778-1.7450.17741440.15782910X-RAY DIFFRACTION100
1.745-1.82430.17291480.1592890X-RAY DIFFRACTION100
1.8243-1.92040.20761420.16232894X-RAY DIFFRACTION100
1.9204-2.04060.19331450.15882904X-RAY DIFFRACTION100
2.0406-2.1980.18941480.15672930X-RAY DIFFRACTION100
2.198-2.41890.18531450.15712914X-RAY DIFFRACTION100
2.4189-2.76810.19081520.16572933X-RAY DIFFRACTION100
2.7681-3.48440.19331360.172900X-RAY DIFFRACTION98
3.4844-19.7860.18811250.16462458X-RAY DIFFRACTION82
Refinement TLS params.Method: refined / Origin x: -8.99 Å / Origin y: -1.679 Å / Origin z: 16.1471 Å
111213212223313233
T0.0195 Å20.001 Å20.0038 Å2-0.0186 Å20.002 Å2--0.0229 Å2
L0.3171 °2-0.0543 °20.1352 °2-0.2263 °2-0.0396 °2--0.2514 °2
S0.0125 Å °-0.0055 Å °0.0711 Å °-0.0093 Å °-0.0191 Å °0.0062 Å °0.0111 Å °0.0364 Å °-0.0044 Å °
Refinement TLS groupSelection details: all

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