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- PDB-1eou: CRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH A... -

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Basic information

Entry
Database: PDB / ID: 1eou
TitleCRYSTAL STRUCTURE OF HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH AN ANTICONVULSANT SUGAR SULFAMATE
ComponentsCARBONIC ANHYDRASE II (CA II)
KeywordsLYASE / HYDROLASE / CO2 HYDRATION / PROTEIN-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 / positive regulation of synaptic transmission, GABAergic ...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 / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / 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-SMS / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRecacha, R. / Costanzo, M.J. / Maryanoff, B.E. / Chattopadhyay, D.
Citation
Journal: Biochem.J. / Year: 2002
Title: Crystal structure of human carbonic anhydrase II complexed with an anti-convulsant sugar sulphamate.
Authors: Recacha, R. / Costanzo, M.J. / Maryanoff, B.E. / Chattopadhyay, D.
#1: Journal: J.Am.Chem.Soc. / Year: 1997
Title: Novel Binding Mode of Hydroxamate Inhibitors to Human Carbonic Anhydrase II
Authors: Scolnick, L.R. / Clements, A.M. / Christianson, D.W.
#2: Journal: J.Med.Chem. / Year: 1998
Title: tructure-Activity Studies on Anticonvulsant Sugar Sulfamates Related to Topiramate. Enhanced Potency with Cyclic Sulfate Derivatives
Authors: Maryanoff, B.E. / Costanzo, M.J. / Nortey, S.O. / Greco, M.N. / Shank, R.P.
History
DepositionMar 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 7, 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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE II (CA II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7163
Polymers29,2891
Non-polymers4272
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.275, 41.390, 72.509
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a human carbonic anhydrase monomer complexed with a zinc ion and the inhibitor RWJ-37947

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Components

#1: Protein CARBONIC ANHYDRASE II (CA II)


Mass: 29289.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: ERYTHROCYTES / Cellular location: CYTOPLASMERYTHROCYTES / 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 / Details: RWJ-37947 is a synthetic inhibitor
#3: Chemical ChemComp-SMS / SULFAMIC ACID 2,3-O-(1-METHYLETHYLIDENE)-4,5-O-SULFONYL-BETA-FRUCTOPYRANOSE ESTER


Mass: 361.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO10S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: TRIS.HCl, smmonium sulfate, dithiothreitol, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
24 mMdithiothreitol1drop
32.8 Mammonium sulfate1reservoir
450 mMTris-HCl1reservoirpH8.8

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 15663 / Num. obs: 14360 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Num. unique all: 16971 / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 16971 / Num. measured all: 169841
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 77.2 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→14.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1327714.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1338 10.2 %RANDOM
Rwork0.176 ---
obs0.176 13084 90.9 %-
all-15663 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.85 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20.3 Å2
2---1.41 Å20 Å2
3---2.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 23 179 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it0.681.5
X-RAY DIFFRACTIONc_mcangle_it1.112
X-RAY DIFFRACTIONc_scbond_it1.012
X-RAY DIFFRACTIONc_scangle_it1.492.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 205 10.1 %
Rwork0.174 1825 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2INH.PARAMINH.TOP
X-RAY DIFFRACTION3ZN.PARAMTOPH19.ION
X-RAY DIFFRACTION4WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 13549 / σ(I): 0 / σ(F): 3 / % reflection Rfree: 10.2 % / Rfactor obs: 0.018 / Rfactor Rfree: 0.023
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it0.681.5
X-RAY DIFFRACTIONc_scbond_it1.012
X-RAY DIFFRACTIONc_mcangle_it1.112
X-RAY DIFFRACTIONc_scangle_it1.492.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.248 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.174

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