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- PDB-2cbd: STRUCTURE OF NATIVE AND APO CARBONIC ANHYDRASE II AND SOME OF ITS... -

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Basic information

Entry
Database: PDB / ID: 2cbd
TitleSTRUCTURE OF NATIVE AND APO CARBONIC ANHYDRASE II AND SOME OF ITS ANION-LIGAND COMPLEXES
ComponentsCARBONIC ANHYDRASE II
KeywordsLYASE(OXO-ACID)
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
SULFITE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsHakansson, K. / Carlsson, M. / Svensson, L.A. / Liljas, A.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of native and apo carbonic anhydrase II and structure of some of its anion-ligand complexes.
Authors: Hakansson, K. / Carlsson, M. / Svensson, L.A. / Liljas, A.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Structure of Cobalt Carbonic Anhydrase Complexed with Bicarbonate
Authors: Hakansson, K. / Wehnert, A.
History
DepositionJun 1, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET SHEET B1 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET ...SHEET SHEET B1 OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS *B1A* AND *B1B* ARE DEFINED. STRANDS 5, 6, 7, 8, 9, AND 10 OF B1A ARE IDENTICAL TO STRANDS 2, 3, 4, 5, 6, AND 7 OF B1B, RESPECTIVELY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3293
Polymers29,1841
Non-polymers1452
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.700, 41.700, 73.000
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 4, 14, 64, AND 136 ARE DISORDERED AND ARE PRESENTED WITH TWO ALTERNATE CONFORMATIONS IN THIS ENTRY.
2: RESIDUES 30 AND 202 ARE CIS PROLINES.

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Components

#1: Protein CARBONIC ANHYDRASE II


Mass: 29183.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer detailsCARBONIC ANHYDRASE CONTAINS ONE ZINC ION PER POLYPEPTIDE CHAIN, WITH RESIDUE NUMBER 262 AND A ...CARBONIC ANHYDRASE CONTAINS ONE ZINC ION PER POLYPEPTIDE CHAIN, WITH RESIDUE NUMBER 262 AND A BISULFITE ANION WITH RESIDUE NUMBER 500.
Sequence detailsRESIDUES 125 AND 127 ARE ADJACENT IN THE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal grow
*PLUS
pH: 8.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.4 Mammonium sulfate11
250 mMTris-HCl11
31 mM11HgCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.67 Å / Lowest resolution: 3.04 Å / Num. all: 29292 / Num. obs: 26190 / % possible obs: 89.4 % / Num. measured all: 71794 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.67 Å / Lowest resolution: 1.78 Å / % possible obs: 89.4 % / Num. possible: 4835 / Num. unique obs: 2540 / Num. measured obs: 4080 / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 43.8

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.67→10 Å /
RfactorNum. reflection
obs0.152 26190
Refinement stepCycle: LAST / Resolution: 1.67→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 5 217 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.051
X-RAY DIFFRACTIONp_mcangle_it1.6891.5
X-RAY DIFFRACTIONp_scbond_it2.2611.5
X-RAY DIFFRACTIONp_scangle_it3.5752
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.2340.15
X-RAY DIFFRACTIONp_singtor_nbd0.1590.2
X-RAY DIFFRACTIONp_multtor_nbd0.1590.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1440.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.73
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor30.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.67 Å / Lowest resolution: 10 Å / Num. reflection obs: 26190 / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.4 Å2

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