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- PDB-8b29: Human carbonic anhydrase II containing 6-fluorotryptophanes. -

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Basic information

Entry
Database: PDB / ID: 8b29
TitleHuman carbonic anhydrase II containing 6-fluorotryptophanes.
ComponentsCarbonic anhydrase 2
KeywordsLYASE
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, 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPham, L.B.T. / Costantino, A. / Barbieri, L. / Calderone, V. / Luchinat, E. / Banci, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Direct Expression of Fluorinated Proteins in Human Cells for 19 F In-Cell NMR Spectroscopy.
Authors: Pham, L.B.T. / Costantino, A. / Barbieri, L. / Calderone, V. / Luchinat, E. / Banci, L.
History
DepositionSep 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2622
Polymers29,1971
Non-polymers651
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.200, 41.220, 71.960
Angle α, β, γ (deg.)90.000, 104.330, 90.000
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
Details: All tryptophanes in the structure are replaced by 6-fluorotryptophanes
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Homo sapiens (human)
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.9 M ammonium sulfate, 0.1 M Tris-HCl

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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: Jul 27, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.7→32 Å / Num. obs: 23397 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.7
Reflection shellResolution: 1.701→1.761 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Num. unique obs: 2385 / CC1/2: 0.59

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CA2

1ca2


Resolution: 1.7→31.98 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1170 5 %
Rwork0.1623 22226 -
obs0.1647 23396 87.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.11 Å2 / Biso mean: 15.3913 Å2 / Biso min: 4.44 Å2
Refinement stepCycle: final / Resolution: 1.7→31.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 1 288 2354
Biso mean--10.72 22.85 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.780.2952880.23861687177554
1.78-1.870.26581100.2112090220066
1.87-1.990.24671360.17512579271583
1.99-2.140.22681660.16631553321100
2.14-2.360.22581660.160531483314100
2.36-2.70.22251660.17531543320100
2.7-3.40.20011670.159331783345100
3.4-31.980.17151710.1383235340699
Refinement TLS params.Method: refined / Origin x: 11.6251 Å / Origin y: -0.3899 Å / Origin z: 16.0034 Å
111213212223313233
T0.039 Å2-0.0005 Å20.0006 Å2-0.0386 Å20.0032 Å2--0.0456 Å2
L0.4942 °2-0.0199 °20.0144 °2-0.4347 °2-0.0687 °2--0.6257 °2
S-0.008 Å °-0.0156 Å °0.0119 Å °-0.0321 Å °0.0066 Å °0.0085 Å °-0.0095 Å °0.0157 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 301
2X-RAY DIFFRACTION1allS1 - 372

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