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

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Basic information

Entry
Database: PDB / ID: 3oil
TitleHuman Carbonic anhydrase II mutant A65S, N67Q (CA IX mimic) 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / 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-VZ5 / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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_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)29,7643
Polymers29,3191
Non-polymers4452
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.138, 41.256, 71.570
Angle α, β, γ (deg.)90.00, 104.07, 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 40.24 %
Crystal growTemperature: 298 K / 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
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 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: 36899 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.28 Å2 / Rsym value: 0.025 / Net I/σ(I): 48.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 14.7 / Rsym value: 0.09 / % possible all: 91.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.6_3_467model 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→23.14 Å / SU ML: 0.21 / Isotropic thermal model: TLS / σ(F): 0 / Phase error: 14.31 / Stereochemistry target values: ML
Details: INDIVIDUAL COORDINATE, INDIVIDUAL ISOTROPIC ADP, TLS, OCCUPANCY, HYDROGEN WRITING
RfactorNum. reflection% reflection
Rfree0.173 1850 5.01 %
Rwork0.144 --
obs0.145 36899 95.6 %
all-36986 -
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.86 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso mean: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.0792 Å2-0 Å2-0.0125 Å2
2---1.2136 Å20 Å2
3---0.1344 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 27 371 2449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122353
X-RAY DIFFRACTIONf_angle_d1.5063241
X-RAY DIFFRACTIONf_dihedral_angle_d16.658949
X-RAY DIFFRACTIONf_chiral_restr0.085345
X-RAY DIFFRACTIONf_plane_restr0.008422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53890.31311370.30572500X-RAY DIFFRACTION89
1.5389-1.58420.25031300.2272624X-RAY DIFFRACTION93
1.5842-1.63530.19781460.17652621X-RAY DIFFRACTION94
1.6353-1.69370.18511520.15162633X-RAY DIFFRACTION95
1.6937-1.76150.18241460.13292679X-RAY DIFFRACTION95
1.7615-1.84160.16941410.12442700X-RAY DIFFRACTION96
1.8416-1.93870.15871290.13012714X-RAY DIFFRACTION97
1.9387-2.06010.18511330.13832754X-RAY DIFFRACTION98
2.0601-2.2190.16151430.14182756X-RAY DIFFRACTION97
2.219-2.44210.15741470.12772789X-RAY DIFFRACTION99
2.4421-2.7950.15771670.13152783X-RAY DIFFRACTION99
2.795-3.51940.17331430.1342812X-RAY DIFFRACTION98
3.5194-23.14410.16041360.14732684X-RAY DIFFRACTION92
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)
10.0086-0.0039-0.005-0.0020.00390.0141-0.10140.0318-0.19690.0088-0.0591-0.24990.02490.188-00.09570.00280.0480.16450.01620.21237.088-5.231411.5381
20.169-0.21150.26840.3729-0.4150.4364-0.1136-0.16480.01750.10090.096-0.12650.03220.0199-0.01360.04590.00920.01030.1012-0.01040.0728-3.2132-3.090527.1108
30.11740.03410.130.3056-0.01070.14770.0111-0.03350.0572-0.13390.0160.1328-0.124-0.009900.13920.0004-0.01560.11240.02380.144-17.10626.945813.0311
40.346-0.07050.02780.63650.1210.4365-0.00250.0041-0.0047-0.11690.0235-0.0036-0.01880.017600.0746-0.0057-0.00030.06190.00370.0598-10.154-3.75813.0758
50.0233-0.04410.01140.0549-0.00620.0163-0.0975-0.3475-0.03440.18220.1217-0.0010.04920.018600.11510.02180.01110.1819-0.00160.0869-10.2156-3.191234.4375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:9)
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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