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- PDB-3oim: Human Carbonic anhydrase II bound by 2-Ethylestradiol 3-O-sulfamate -

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Basic information

Entry
Database: PDB / ID: 3oim
TitleHuman Carbonic anhydrase II bound by 2-Ethylestradiol 3-O-sulfamate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / 2-ethylestrone / estradiol / sulfamate / mixed alpha-beta / Carbon Dioxide/Bicarbonate conversion
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-VZ5 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R.
Citation
Journal: LETT.DRUG DES.DISCOVERY / Year: 2011
Title: Characterization of Carbonic Anhydrase Isozyme Specific Inhibition by Sulfamated 2-Ethylestra Compounds
Authors: Sippel, K.H. / Stander, B.A. / Robbins, A.H. / Tu, C.K. / Agbandje-McKenna, M. / Silverman, D.N. / Joubert, A.M. / McKenna, R.
#1: Journal: Biochemistry / Year: 2010
Title: Structures of human carbonic anhydrase II/inhibitor complexes reveal a second binding site for steroidal and nonsteroidal inhibitors.
Authors: Cozier, G.E. / Leese, M.P. / Lloyd, M.D. / Baker, M.D. / Thiyagarajan, N. / Acharya, K.R. / Potter, B.V.
#2: Journal: Biochemistry / Year: 2009
Title: Design of a carbonic anhydrase IX active-site mimic to screen inhibitors for possible anticancer properties.
Authors: Genis, C. / Sippel, K.H. / Case, N. / Cao, W. / Avvaru, B.S. / Tartaglia, L.J. / Govindasamy, L. / Tu, C. / Agbandje-McKenna, M. / Silverman, D.N. / Rosser, C.J. / McKenna, R.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)29,9045
Polymers29,2891
Non-polymers6154
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.187, 41.240, 71.341
Angle α, β, γ (deg.)90.00, 103.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 307 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VZ5 / (14beta,17alpha)-2-ethyl-17-hydroxyestra-1(10),2,4-trien-3-yl sulfamate


Mass: 379.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO4S
#4: 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
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M Sodium Citrate, 100 mM Tris, 7.5 mM 2-Ethylestradiol 3-O-sulfamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 5, 2010 / Details: osmic mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 39949 / Num. obs: 39564 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.045 / Net I/σ(I): 29.8
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.45-1.53.54.50.268177.9
1.5-1.564.57.50.203192.6
1.56-1.634.410.80.142193.5
1.63-1.724.414.30.105194.2
1.72-1.834.5200.075194
1.83-1.974.5250.056195.2
1.97-2.174.528.40.05197.1
2.17-2.484.6310.045198
2.48-3.124.732.80.042199.1
3.12-504.632.20.04199.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.6.3_467)model building
PHENIX(phenix.refine: 1.6.3_467)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.3_467phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ili

2ili


Resolution: 1.45→23.763 Å / SU ML: 0.2 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 14.65 / Stereochemistry target values: ML
Details: Individual coordinate, individual isotropic ADP, TLS, occupancy, hydrogen writing
RfactorNum. reflection% reflection
Rfree0.1698 1985 5.02 %
Rwork0.1444 --
obs0.1457 39564 93.18 %
all-39949 -
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.403 Å2 / ksol: 0.483 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2834 Å2-0 Å2-0.8785 Å2
2---1.4373 Å20 Å2
3---1.1539 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 37 303 2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132374
X-RAY DIFFRACTIONf_angle_d1.6973264
X-RAY DIFFRACTIONf_dihedral_angle_d13.636917
X-RAY DIFFRACTIONf_chiral_restr0.091339
X-RAY DIFFRACTIONf_plane_restr0.011429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48610.4988930.48851960X-RAY DIFFRACTION69
1.4861-1.52630.37461360.37732557X-RAY DIFFRACTION89
1.5263-1.57120.32161370.29282595X-RAY DIFFRACTION91
1.5712-1.62190.30281440.21582629X-RAY DIFFRACTION92
1.6219-1.67990.17181390.16572677X-RAY DIFFRACTION93
1.6799-1.74710.19751370.132674X-RAY DIFFRACTION94
1.7471-1.82660.17661420.1262682X-RAY DIFFRACTION94
1.8266-1.92290.15071430.1242727X-RAY DIFFRACTION94
1.9229-2.04330.18041530.13082759X-RAY DIFFRACTION96
2.0433-2.2010.16171350.13122786X-RAY DIFFRACTION97
2.201-2.42220.13811540.12292835X-RAY DIFFRACTION98
2.4222-2.77230.17441530.12372854X-RAY DIFFRACTION99
2.7723-3.4910.15271580.12582885X-RAY DIFFRACTION99
3.491-23.76570.14221610.14222959X-RAY DIFFRACTION99
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)
10.0620.0031-0.0050.017-0.00050.0703-0.01890.1334-0.2261-0.1915-0.1443-0.7730.02230.4171-0.00010.1605-0.00950.05830.23810.01120.29298.1353-4.512510.6682
20.52540.07330.53820.862-0.32540.7795-0.1227-0.2665-0.04740.12650.0901-0.0644-0.02020.0289-0.00010.11780.02010.01270.15470.00470.114-3.9835-2.864227.4936
30.15350.11370.12860.3305-0.0420.34240.0593-0.01390.1256-0.1038-0.00780.0882-0.1727-0.0484-0.00010.1830.007-0.01140.14660.01010.1849-16.69786.773812.842
40.7102-0.0540.09280.76650.13990.97730.00270.0289-0.0271-0.11820.01460.0224-0.00560.027800.0989-0.0059-0.00210.09180.00630.0986-10.2029-3.619113.3621
50.0442-0.06110.02230.1119-0.00260.08370.0451-0.6772-0.02220.22430.07980.01690.0386-0.05560.00010.17390.00270.01410.2777-0.0010.1512-11.5222-3.626634.6733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:9)
2X-RAY DIFFRACTION2(chain A and resid 10:45)
3X-RAY DIFFRACTION3(chain A and resid 46:87)
4X-RAY DIFFRACTION4(chain A and resid 88:251)
5X-RAY DIFFRACTION5(chain A and resid 252:261)

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