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- PDB-9oam: Room temperature structure of carbonic anhydrase II in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9oam
TitleRoom temperature structure of carbonic anhydrase II in complex with vorinostat (co-crystal)
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase II / Vorinostat / Inhibitor Complex / Zinc Binding Protein
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / cytoplasm / cytosol
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
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGulkis, M.C. / McKenna, R. / Fisher, S.Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Off-target binding of the histone deacetylase inhibitor vorinostat to carbonic anhydrase II and IX.
Authors: Gulkis, M.C. / Hodgkinson, J.T. / Sele, C.P. / Knecht, W. / McKenna, R. / Fisher, S.Z.
History
DepositionApr 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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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)29,6193
Polymers29,2891
Non-polymers3302
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.912, 41.753, 72.780
Angle α, β, γ (deg.)90.000, 104.496, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#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 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / 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-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 50 mM Tris HCl pH 8.0, 1.25 M sodium citrate / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.4→24.88 Å / Num. obs: 49387 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.47 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.048 / Net I/σ(I): 10
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4152 / CC1/2: 0.832 / Rpim(I) all: 0.23 / % possible all: 84.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.07 Å / SU ML: 0.1163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.966
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1707 3773 4.11 %
Rwork0.1525 88100 -
obs0.1532 48422 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 20 230 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612190
X-RAY DIFFRACTIONf_angle_d0.92392973
X-RAY DIFFRACTIONf_chiral_restr0.0864306
X-RAY DIFFRACTIONf_plane_restr0.0071387
X-RAY DIFFRACTIONf_dihedral_angle_d12.4465809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.21021160.23912571X-RAY DIFFRACTION75.82
1.42-1.440.2132960.23092768X-RAY DIFFRACTION79.07
1.44-1.460.27441420.23232915X-RAY DIFFRACTION86.75
1.46-1.480.26311310.22273309X-RAY DIFFRACTION95.11
1.48-1.50.21321200.22453312X-RAY DIFFRACTION96.73
1.5-1.520.221770.20083268X-RAY DIFFRACTION97.79
1.52-1.550.21411290.20173325X-RAY DIFFRACTION96.48
1.55-1.570.19991320.18883302X-RAY DIFFRACTION97.01
1.57-1.60.21481460.18483268X-RAY DIFFRACTION95.82
1.6-1.630.2091590.17483282X-RAY DIFFRACTION96.52
1.63-1.670.17541390.17153398X-RAY DIFFRACTION97.82
1.67-1.70.18781410.17453336X-RAY DIFFRACTION97.72
1.7-1.740.19391560.16343347X-RAY DIFFRACTION97.22
1.74-1.790.21951360.1623317X-RAY DIFFRACTION97.4
1.79-1.830.19331440.15733296X-RAY DIFFRACTION97.26
1.83-1.890.16451520.15453346X-RAY DIFFRACTION97.76
1.89-1.950.15211320.15623380X-RAY DIFFRACTION97.91
1.95-2.020.15331470.14883306X-RAY DIFFRACTION97.63
2.02-2.10.16881450.14533302X-RAY DIFFRACTION96.99
2.1-2.190.16071510.14683365X-RAY DIFFRACTION97.05
2.19-2.310.18051230.14483317X-RAY DIFFRACTION97.15
2.31-2.450.16321410.15113341X-RAY DIFFRACTION97.67
2.45-2.640.17891470.15213319X-RAY DIFFRACTION97.14
2.64-2.910.15961350.1523359X-RAY DIFFRACTION98.28
2.91-3.330.14731520.14123371X-RAY DIFFRACTION98.57
3.33-4.190.14871410.12263362X-RAY DIFFRACTION98.07
4.19-19.070.14771430.12633318X-RAY DIFFRACTION96.95

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