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- PDB-4m2w: Genetically engineered Carbonic Anhydrase IX in complex with Dorz... -

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Basic information

Entry
Database: PDB / ID: 4m2w
TitleGenetically engineered Carbonic Anhydrase IX in complex with Dorzolamide
ComponentsCarbonic anhydrase 2
KeywordsLyase/Lyase Inhibitor / Carbonic Anhydrase IX mimic / 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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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-ETS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.658 Å
AuthorsPinard, M.P. / Boone, C.D. / Rife, B.D. / Supuran, C.T. / McKenna, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Structural study of interaction between brinzolamide and dorzolamide inhibition of human carbonic anhydrases.
Authors: Pinard, M.A. / Boone, C.D. / Rife, B.D. / Supuran, C.T. / McKenna, R.
History
DepositionAug 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2343
Polymers28,8441
Non-polymers3902
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.609, 41.796, 72.900
Angle α, β, γ (deg.)90.000, 104.010, 90.000
Int Tables number4
Space group name H-MP1211
DetailsNo symmetry operations

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Components

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


Mass: 28844.465 Da / Num. of mol.: 1 / Mutation: A65S, N67Q, E69T, I91L, F130V, K169E, L203A
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-ETS / (4S-TRANS)-4-(ETHYLAMINO)-5,6-DIHYDRO-6-METHYL-4H-THIENO(2,3-B)THIOPYRAN-2-SULFONAMIDE-7,7-DIOXIDE / Dorzolamide


Mass: 324.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O4S3 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Drops were prepared by mixing 7 uL of the final concentrated protein (~10 mg/mL) and 3 uL of precipitant solution against 1 mL of precipitant solution. The precipitant solution conditions ...Details: Drops were prepared by mixing 7 uL of the final concentrated protein (~10 mg/mL) and 3 uL of precipitant solution against 1 mL of precipitant solution. The precipitant solution conditions varied, and consisted of 50 mM Tris-HCl (pH 7.5) and 1.6 M sodium citrate, 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 / Date: Jun 8, 2012
RadiationMonochromator: Varimax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.658→20 Å / Num. obs: 27938 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.01 Å2
Reflection shellResolution: 1.66→1.72 Å / % possible all: 90.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.658→18.961 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.9246 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 13.77 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1524 1396 5 %Random 5%
Rwork0.1302 ---
all0.1314 ---
obs0.1314 27924 93.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.5 Å2 / Biso mean: 25.7071 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: LAST / Resolution: 1.658→18.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 20 81 2143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092191
X-RAY DIFFRACTIONf_angle_d1.3372994
X-RAY DIFFRACTIONf_chiral_restr0.076312
X-RAY DIFFRACTIONf_plane_restr0.008389
X-RAY DIFFRACTIONf_dihedral_angle_d17.855828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6577-1.71690.17691280.14142431255987
1.7169-1.78560.17711330.13382568270191
1.7856-1.86680.14811300.12322588271892
1.8668-1.96510.14511390.11792585272492
1.9651-2.08810.15031390.11752645278493
2.0881-2.24910.16511430.12112636277994
2.2491-2.4750.16011360.13062718285495
2.475-2.83210.17511470.14082730287796
2.8321-3.56430.18171460.14872773291997
3.5643-18.96210.11781550.12192854300998
Refinement TLS params.Method: refined / Origin x: 11.7666 Å / Origin y: -1.8722 Å / Origin z: 16.208 Å
111213212223313233
T0.0698 Å2-0.0066 Å20.002 Å2-0.0681 Å20.0053 Å2--0.077 Å2
L1.1949 °2-0.056 °2-0.0264 °2-0.8713 °2-0.1107 °2--1.1534 °2
S-0.0112 Å °0.0037 Å °0.0432 Å °-0.0213 Å °0.0154 Å °-0.0136 Å °0.0196 Å °0.0089 Å °0.0008 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allA262 - 301
3X-RAY DIFFRACTION1allA1 - 441
4X-RAY DIFFRACTION1allC1 - 49
5X-RAY DIFFRACTION1allA1 - 302

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