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- PDB-8p6u: Human carbonic anhydrase II containing 5-fluorotryptophanes -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8p6u
TitleHuman carbonic anhydrase II containing 5-fluorotryptophanes
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Human carbonic anhydrase II / hCAII / 5-fluorotryptophane / in-cell NMR
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 / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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, 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
BENZOIC ACID / 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
DepositionMay 30, 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)29,7064
Polymers29,1971
Non-polymers5093
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-40 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.850, 41.280, 71.720
Angle α, β, γ (deg.)90.00, 104.10, 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: 29196.727 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.9M 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: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. obs: 56391 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.46
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3 / Num. unique obs: 4094 / CC1/2: 0.93

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→20.9 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1753 2818 5 %
Rwork0.1443 --
obs0.1458 56383 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→20.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 20 308 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142145
X-RAY DIFFRACTIONf_angle_d1.4742913
X-RAY DIFFRACTIONf_dihedral_angle_d20.986283
X-RAY DIFFRACTIONf_chiral_restr0.104300
X-RAY DIFFRACTIONf_plane_restr0.012377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.2841350.18882570X-RAY DIFFRACTION93
1.32-1.350.23641400.18062656X-RAY DIFFRACTION96
1.35-1.370.20011420.16342699X-RAY DIFFRACTION97
1.37-1.40.19991420.15142698X-RAY DIFFRACTION98
1.4-1.430.19871450.152742X-RAY DIFFRACTION99
1.43-1.460.18161420.14312723X-RAY DIFFRACTION99
1.46-1.50.19941460.14112785X-RAY DIFFRACTION100
1.5-1.540.21181460.13942760X-RAY DIFFRACTION100
1.54-1.590.15411450.13862766X-RAY DIFFRACTION100
1.59-1.640.16931460.12892766X-RAY DIFFRACTION100
1.64-1.70.16961420.13022704X-RAY DIFFRACTION98
1.7-1.760.15911370.12442606X-RAY DIFFRACTION93
1.76-1.840.16141280.1312422X-RAY DIFFRACTION87
1.84-1.940.16261380.13262620X-RAY DIFFRACTION95
1.94-2.060.15961420.13612708X-RAY DIFFRACTION97
2.06-2.220.17311420.13962696X-RAY DIFFRACTION96
2.22-2.450.1641410.14562672X-RAY DIFFRACTION95
2.45-2.80.2071380.15842635X-RAY DIFFRACTION94
2.8-3.520.1661370.15442595X-RAY DIFFRACTION92
3.52-20.90.14761440.14042742X-RAY DIFFRACTION95

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