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- PDB-1bv3: HUMAN CARBONIC ANHYDRASE II COMPLEXED WITH UREA -

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Basic information

Entry
Database: PDB / ID: 1bv3
TitleHUMAN CARBONIC ANHYDRASE II COMPLEXED WITH UREA
ComponentsPROTEIN (CARBONIC ANHYDRASE II)
KeywordsLYASE / CARBONATE HYDRO-LYASE
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
4-(HYDROXYMERCURY)BENZOIC ACID / UREA / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.85 Å
AuthorsBriganti, F. / Mangani, S. / Scozzafava, A. / Vernaglione, G. / Supuran, C.T.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1999
Title: Carbonic anhydrase catalyzes cyanamide hydration to urea: is it mimicking the physiological reaction?
Authors: Briganti, F. / Mangani, S. / Scozzafava, A. / Vernaglione, G. / Supuran, C.T.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6224
Polymers29,1581
Non-polymers4643
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.820, 42.020, 73.030
Angle α, β, γ (deg.)90.00, 104.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (CARBONIC ANHYDRASE II) / HCA II


Mass: 29157.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: ERYTHROCYTES / Plasmid: PACA-HCA II / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6HgO3
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growpH: 7.7
Details: 2.3M AMMONIUM SULFATE, 55MM TRIS-HCL, 1MM SODIUM 4-(HYDROXYMERCURY)BENZOATE, PH 7, pH 7.7
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of enzyme and reservoir solutions
PH range low: 7.8 / PH range high: 7.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
250 mMTris-HCl1drop
31 mMsodium 4-(hydroxymercury)benzoate1drop
42.3-2.4 Mammonium sulfate1reservoir
550 mMTris-HCl1reservoir
61 mMsodium 4-(hydroxymercury)benzoate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: CCD / Date: May 15, 1998 / Details: MIRRORS
RadiationMonochromator: GOBEL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 21668 / % possible obs: 91.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 4.8 / % possible all: 92.5
Reflection
*PLUS
Num. measured all: 55987
Reflection shell
*PLUS
% possible obs: 92.5 % / Mean I/σ(I) obs: 5

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
CCP4model building
CCP4refinement
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.85→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE SIDE CHAIN OF HIS A 64 IS DISORDERED WITH AN OCCUPANCY OF 0.70.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1068 5 %RANDOM
Rwork0.171 ---
all-21358 --
obs-21358 91.8 %-
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 15 137 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0770.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.833
X-RAY DIFFRACTIONp_mcangle_it3.575
X-RAY DIFFRACTIONp_scbond_it6.587
X-RAY DIFFRACTIONp_scangle_it8.7210
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1850.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2060.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.3
X-RAY DIFFRACTIONp_planar_tor3.33
X-RAY DIFFRACTIONp_staggered_tor19.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.720
X-RAY DIFFRACTIONp_special_tor1215
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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