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- PDB-3oik: Human Carbonic anhydrase II mutant A65S, N67Q (CA IX mimic) bound... -

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Basic information

Entry
Database: PDB / ID: 3oik
TitleHuman Carbonic anhydrase II mutant A65S, N67Q (CA IX mimic) bound by 2-Ethylestradiol 3,17-O,O-bis-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 / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
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-WZB / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)29,9354
Polymers29,3191
Non-polymers6163
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.238, 41.322, 72.201
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29319.086 Da / Num. of mol.: 1 / Mutation: A65S, N67Q
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-WZB / (9BETA,13ALPHA,14BETA,17ALPHA)-2-ETHYLESTRA-1(10),2,4-TRIENE-3,17-DIYL DISULFAMATE / 2-ETHYLESTRADIOL 3,17-O,O-BIS-SULFAMATE


Mass: 458.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N2O6S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 298 K / pH: 9
Details: 1.4 M Sodium Citrate, 100 mM Tris, 7.5 mM 2-Ethylestradiol 3,17-O,O-bis-sulfamate, pH 9.0, 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
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 7, 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: 1.5→50 Å / Num. obs: 35886 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 25.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.39 / % possible all: 89.3

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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: 1.5→25.317 Å / SU ML: 0.19 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 14.95 / Stereochemistry target values: ML
Details: INDIVIDUAL COORDINATE, INDIVIDUAL ISOTROPIC ADP, TLS, OCCUPANCY, HYDROGEN WRITING
RfactorNum. reflection% reflection
Rfree0.1633 1985 5.53 %
Rwork0.1349 --
obs0.1365 35886 92.15 %
all-36402 -
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.45 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 16.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.9687 Å2-0 Å2-0.1521 Å2
2---0.7268 Å20 Å2
3---1.6955 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 37 359 2457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142393
X-RAY DIFFRACTIONf_angle_d1.6033296
X-RAY DIFFRACTIONf_dihedral_angle_d14.424945
X-RAY DIFFRACTIONf_chiral_restr0.114347
X-RAY DIFFRACTIONf_plane_restr0.01426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55320.34091780.3073108X-RAY DIFFRACTION85
1.5532-1.61540.23811880.20533154X-RAY DIFFRACTION87
1.6154-1.68890.21641900.16063212X-RAY DIFFRACTION87
1.6889-1.77790.19931900.13233217X-RAY DIFFRACTION89
1.7779-1.88930.13981890.1213370X-RAY DIFFRACTION91
1.8893-2.03510.1682030.12933437X-RAY DIFFRACTION94
2.0351-2.23980.15832060.12643475X-RAY DIFFRACTION95
2.2398-2.56370.13422090.11763578X-RAY DIFFRACTION97
2.5637-3.22890.15722140.12533603X-RAY DIFFRACTION98
3.2289-25.32020.14332180.1263747X-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)
10.0654-0.01740.0210.0047-0.00320.0491-0.04770.0624-0.1221-0.0175-0.0894-0.1642-0.03760.1685-0.00660.1133-0.00030.05050.12810.01540.16167.622-4.759810.8168
20.2277-0.01680.11950.1741-0.21140.2889-0.086-0.1585-0.0830.09490.0372-0.11070.01340.0635-0.00410.07370.01220.01260.1063-0.00070.0641-3.6615-3.565427.4479
30.10790.07210.12380.14470.02540.11980.01070.00040.1085-0.079-0.02140.0572-0.0824-0.026700.09620.0079-0.00910.08940.00420.1216-16.83416.529213.2992
40.4907-0.0477-0.02910.2107-0.02220.38230.00170.0003-0.0034-0.04060.00310.00590.00670.0033-00.0551-0.0024-0.00160.03870.00180.0465-10.3368-3.688113.5239
50.1186-0.0294-0.03450.16790.07340.3126-0.0274-0.1875-0.00360.09110.1057-0.01420.13960.00740.11370.09910.00540.01230.14230.00430.0851-12.0686-3.561334.6073
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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