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- PDB-8phl: Human carbonic anhydrase II containing 4-fluorophenylalanine -

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Basic information

Entry
Database: PDB / ID: 8phl
TitleHuman carbonic anhydrase II containing 4-fluorophenylalanine
ComponentsCarbonic anhydrase 2
KeywordsLYASE / hCAII / carbonic anhydrase / 4-fluorophenylalanine
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPham, L.B.T. / Costantino, A. / Barbieri, L. / Calderone, V. / Luchinat, E. / Banci, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
Citation
Journal: Protein Sci. / Year: 2024
Title: Controlling the incorporation of fluorinated amino acids in human cells and its structural impact.
Authors: Costantino, A. / Pham, L.B.T. / Barbieri, L. / Calderone, V. / Ben-Nissan, G. / Sharon, M. / Banci, L. / Luchinat, E.
#1: Journal: J Am Chem Soc / Year: 2023
Title: Direct Expression of Fluorinated Proteins in Human Cells for
Authors: Pham, L.B.T. / Costantino, A. / Barbieri, L. / Calderone, V. / Luchinat, E. / Banci, L.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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)29,6743
Polymers29,2871
Non-polymers3872
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-42 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.820, 40.900, 70.870
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29286.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase
#2: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.9 Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.541 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Feb 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.3→31.5 Å / Num. obs: 57104 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4105 / CC1/2: 0.64 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.5 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.85 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19448 2682 5 %RANDOM
Rwork0.17787 ---
obs0.17872 50941 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0.1 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 11 256 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122135
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161950
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6542907
X-RAY DIFFRACTIONr_angle_other_deg0.5841.5894526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.7557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26910353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022449
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0971.3771031
X-RAY DIFFRACTIONr_mcbond_other1.0961.3771031
X-RAY DIFFRACTIONr_mcangle_it1.5312.4711287
X-RAY DIFFRACTIONr_mcangle_other1.532.4741288
X-RAY DIFFRACTIONr_scbond_it1.2371.6061104
X-RAY DIFFRACTIONr_scbond_other1.2371.6091105
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7152.8181621
X-RAY DIFFRACTIONr_long_range_B_refined2.79317.82638
X-RAY DIFFRACTIONr_long_range_B_other2.4916.312535
X-RAY DIFFRACTIONr_rigid_bond_restr4.48234085
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 183 -
Rwork0.261 3464 -
obs--87.21 %

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