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- PDB-4r5a: A Carbonic Anhydrase IX Mimic in Complex with a Carbohydrate-Base... -

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Basic information

Entry
Database: PDB / ID: 4r5a
TitleA Carbonic Anhydrase IX Mimic in Complex with a Carbohydrate-Based Sulfamate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic Anhydrase IX Mimic
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
Chem-3J4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMahon, B.P. / McKenna, R.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural Insights into Carbonic Anhydrase IX Isoform Specificity of Carbohydrate-Based Sulfamates.
Authors: Moeker, J. / Mahon, B.P. / Bornaghi, L.F. / Vullo, D. / Supuran, C.T. / McKenna, R. / Poulsen, S.A.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)29,7924
Polymers29,2421
Non-polymers5503
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.038, 41.429, 72.259
Angle α, β, γ (deg.)90.00, 103.79, 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


Mass: 29241.918 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-3J4 / (6S)-2,6-anhydro-6-{[(3R)-3-(sulfamoyloxy)pyrrolidin-1-yl]sulfonyl}-D-glucitol


Type: L-saccharide / Mass: 392.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20N2O10S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.6 M Sodium Citrate, 50mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→19.96 Å / Num. obs: 29753 / % possible obs: 93.2 % / Redundancy: 2.4 % / Rsym value: 0.062
Reflection shellResolution: 1.64→1.76 Å / % possible all: 87.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KS3
Resolution: 1.64→19.96 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 1479 4.97 %
Rwork0.156 --
obs0.157 28680 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 31 231 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072240
X-RAY DIFFRACTIONf_angle_d1.4063058
X-RAY DIFFRACTIONf_dihedral_angle_d13.974814
X-RAY DIFFRACTIONf_chiral_restr0.056324
X-RAY DIFFRACTIONf_plane_restr0.006394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.68340.25561220.2052465X-RAY DIFFRACTION94
1.6834-1.74360.23431400.17522492X-RAY DIFFRACTION97
1.7436-1.81330.20831290.16472538X-RAY DIFFRACTION97
1.8133-1.89580.20111320.15312537X-RAY DIFFRACTION97
1.8958-1.99570.18941290.1472520X-RAY DIFFRACTION97
1.9957-2.12060.19111310.15052563X-RAY DIFFRACTION98
2.1206-2.28410.18721430.1512589X-RAY DIFFRACTION99
2.2841-2.51350.17371360.15822591X-RAY DIFFRACTION99
2.5135-2.87630.20291340.1622617X-RAY DIFFRACTION100
2.8763-3.62030.17151410.15492645X-RAY DIFFRACTION100
3.6203-19.95790.1661420.14892717X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.9303 Å / Origin y: -1.3104 Å / Origin z: 86.0806 Å
111213212223313233
T0.062 Å2-0.0031 Å20.0054 Å2-0.0639 Å2-0.0038 Å2--0.0682 Å2
L0.6308 °20.0287 °20.1737 °2-0.5722 °2-0.0401 °2--0.7023 °2
S0.0008 Å °-0.019 Å °0.0257 Å °-0.0302 Å °0.019 Å °0.0068 Å °0.0239 Å °0.01 Å °0.002 Å °
Refinement TLS groupSelection details: all

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