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- PDB-6ux1: Carbonic Anhydrase II Complexed with Salicylic Acid -

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Basic information

Entry
Database: PDB / ID: 6ux1
TitleCarbonic Anhydrase II Complexed with Salicylic Acid
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Aspirin Salicylic Acid / Esterase
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
2-HYDROXYBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsAndring, J.T. / Combs, J.E. / McKenna, R.
CitationJournal: Biomolecules / Year: 2020
Title: Aspirin: A Suicide Inhibitor of Carbonic Anhydrase II.
Authors: Andring, J. / Combs, J. / McKenna, R.
History
DepositionNov 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)30,1218
Polymers29,2891
Non-polymers8327
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.427, 41.304, 72.028
Angle α, β, γ (deg.)90.000, 104.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29289.062 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

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Non-polymers , 5 types, 183 molecules

#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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M NaCitrate 50mM Tris pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.355→35.55 Å / Num. obs: 49544 / % possible obs: 94.1 % / Redundancy: 3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.044 / Rrim(I) all: 0.081 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.381.80.787245113450.3280.6431.0230.751.2
7.42-35.553.50.03812293550.9970.0230.04413.399.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.36→35.549 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1668 2002 4.05 %
Rwork0.1544 --
obs0.1549 49449 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.72 Å2 / Biso mean: 24.5433 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.36→35.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 63 176 2298
Biso mean--33.6 30.7 -
Num. residues----258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.36-1.38930.3061860.3447214259
1.3893-1.42690.30421300.2831317288
1.4269-1.46880.25761390.2429341895
1.4688-1.51630.24621450.2147345596
1.5163-1.57050.22421400.2044339795
1.5705-1.63330.21131590.1828348797
1.6333-1.70770.18671440.1742350098
1.7077-1.79770.20061590.1599351097
1.7977-1.91030.18221380.158344296
1.9103-2.05780.15191450.1387358399
2.0578-2.26490.1461630.1379354899
2.2649-2.59250.16331440.14353697
2.5925-3.26590.14251520.1444363299
3.2659-35.5490.14551580.1354362597
Refinement TLS params.Method: refined / Origin x: -30.4684 Å / Origin y: -1.8657 Å / Origin z: 15.8279 Å
111213212223313233
T0.1185 Å2-0.002 Å2-0.0003 Å2-0.1184 Å2-0.0006 Å2--0.1199 Å2
L0.6578 °2-0.079 °20.0167 °2-0.566 °20.0269 °2--0.4691 °2
S-0.0112 Å °-0.037 Å °-0.0036 Å °-0.0314 Å °0.0102 Å °0.0034 Å °0.0175 Å °0.0193 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allC400
4X-RAY DIFFRACTION1allE1 - 183
5X-RAY DIFFRACTION1allD1 - 5
6X-RAY DIFFRACTION1allF1

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