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- PDB-3u3a: structure of Human Carbonic Anhydrase II V143I -

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Basic information

Entry
Database: PDB / ID: 3u3a
Titlestructure of Human Carbonic Anhydrase II V143I
ComponentsCarbonic anhydrase 2
KeywordsLYASE / zinc metalloenzyme / V143I / esterase / site directed mutagenesis / CO2 binding pocket
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 / regulation of intracellular pH / morphogenesis of an epithelium / 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsWest, D. / Mckenna, R.
CitationJournal: To be Published
Title: Structural Analysis of Human Carbonic Anhydrase II Binding Pocket
Authors: West, D. / Mckenna, R. / Robbins, A. / Kim, C. / Tu, C. / Silverman, D. / Gordon, J.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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_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_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
X: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5534
Polymers29,3031
Non-polymers2503
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.216, 41.274, 72.077
Angle α, β, γ (deg.)90.000, 104.240, 90.000
Int Tables number4
Space group name H-MP1211
DetailsEnzyme active as a monomer

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Components

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


Mass: 29303.090 Da / Num. of mol.: 1 / Mutation: V142I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2, HCA2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 40.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M Sodium Citrate 50 mM Tris pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 10, 2010 / Details: mirrors
RadiationMonochromator: Rigaku Varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.549→50 Å / Num. all: 31577 / Num. obs: 31199 / % possible obs: 89.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rsym value: 0.048 / Χ2: 0.964 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.614.60.28329740.858185.4
1.61-1.674.60.20830150.893186.6
1.67-1.754.60.15430460.969187.2
1.75-1.844.60.11431001.066188.2
1.84-1.954.60.08331251.175189.6
1.95-2.14.60.06331560.92190
2.1-2.324.60.05332010.874191.5
2.32-2.654.70.04632500.816191.8
2.65-3.344.60.03933100.956193.6
3.34-504.50.03634001.112193.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TBT

1tbt


Resolution: 1.549→30.533 Å / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.9007 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1989 6.38 %random
Rwork0.1628 ---
all0.1645 31577 --
obs0.1633 31199 88.51 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.293 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 64.49 Å2 / Biso mean: 16.4863 Å2 / Biso min: 6.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.0559 Å2-0 Å2-0.1473 Å2
2---0.3107 Å20 Å2
3---1.3665 Å2
Refinement stepCycle: LAST / Resolution: 1.549→30.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 13 243 2316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062204
X-RAY DIFFRACTIONf_angle_d1.1253006
X-RAY DIFFRACTIONf_chiral_restr0.079317
X-RAY DIFFRACTIONf_plane_restr0.005390
X-RAY DIFFRACTIONf_dihedral_angle_d13.08831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5491-1.58790.35821130.32061864197779
1.5879-1.63080.26891330.26221926205982
1.6308-1.67880.2591400.21631967210785
1.6788-1.73290.21231280.1782023215186
1.7329-1.79490.18041480.15992028217687
1.7949-1.86670.20661270.13772053218088
1.8667-1.95170.16521480.14682082223089
1.9517-2.05460.17041490.15272120226990
2.0546-2.18320.18631460.15882139228591
2.1832-2.35180.19841450.15752125227091
2.3518-2.58830.16771450.15972165231092
2.5883-2.96260.20851480.16422216236493
2.9626-3.73150.17811580.14812225238394
3.7315-30.53910.181610.15742277243894

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