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- PDB-6sfq: Atomic resolution structure of human Carbonic Anhydrase II in com... -

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Basic information

Entry
Database: PDB / ID: 6sfq
TitleAtomic resolution structure of human Carbonic Anhydrase II in complex with (R)-5-phenyloxazolidine-2,4-dione
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / complex / CO2 conversion
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
(5R)-5-phenyl-1,3-oxazolidine-2,4-dione / (4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsGloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Atomic resolution structure of human Carbonic Anhydrase II in complex with (R)-5-phenyloxazolidine-2,4-dione
Authors: Gloeckner, S. / Ngo, K. / Heine, A. / Klebe, G.
History
DepositionAug 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,9098
Polymers29,8071
Non-polymers1,1027
Water4,414245
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-62 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.410, 41.608, 72.135
Angle α, β, γ (deg.)90.000, 104.480, 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

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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: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 7 types, 252 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-7Q1 / (5R)-5-phenyl-1,3-oxazolidine-2,4-dione


Mass: 177.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#7: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Sodium citrate 1.4 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→41.608 Å / Num. obs: 128491 / % possible obs: 97.6 % / Redundancy: 3.61 % / Biso Wilson estimate: 9.54 Å2 / CC1/2: 0.999 / Rsym value: 0.045 / Net I/σ(I): 12.79
Reflection shellResolution: 1→1.06 Å / Redundancy: 3.45 % / Mean I/σ(I) obs: 2.22 / Num. unique obs: 20448 / CC1/2: 0.865 / Rsym value: 0.405 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1→41.06 Å / SU ML: 0.0987 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.6414
RfactorNum. reflection% reflectionSelection details
Rfree0.1468 6424 5 %Random selection of 5 %
Rwork0.1261 ---
obs0.1272 128473 97.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.65 Å2
Refinement stepCycle: LAST / Resolution: 1→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 31 245 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572471
X-RAY DIFFRACTIONf_angle_d0.94123410
X-RAY DIFFRACTIONf_chiral_restr0.0792354
X-RAY DIFFRACTIONf_plane_restr0.0074477
X-RAY DIFFRACTIONf_dihedral_angle_d13.2634911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.31522030.26233874X-RAY DIFFRACTION92.49
1.01-1.020.28042100.24183993X-RAY DIFFRACTION96.73
1.02-1.040.21832130.22564049X-RAY DIFFRACTION97.28
1.04-1.050.22722120.20124011X-RAY DIFFRACTION97.37
1.05-1.060.19272140.17434081X-RAY DIFFRACTION96.76
1.06-1.080.17132060.14653907X-RAY DIFFRACTION96.32
1.08-1.090.13052160.12334097X-RAY DIFFRACTION97.89
1.09-1.110.14482120.11764034X-RAY DIFFRACTION97.99
1.11-1.130.11722180.11064129X-RAY DIFFRACTION97.88
1.13-1.140.12142120.1064032X-RAY DIFFRACTION97.95
1.14-1.160.11392140.10354062X-RAY DIFFRACTION98.21
1.16-1.180.13822150.10474083X-RAY DIFFRACTION98.15
1.18-1.210.12442110.10184026X-RAY DIFFRACTION96.8
1.21-1.230.10982150.1024068X-RAY DIFFRACTION98.35
1.23-1.260.11552160.10324120X-RAY DIFFRACTION98.72
1.26-1.290.12232150.10344074X-RAY DIFFRACTION98.42
1.29-1.320.12122160.10154101X-RAY DIFFRACTION98.27
1.32-1.360.10872150.09924081X-RAY DIFFRACTION98.58
1.36-1.40.13232150.10454102X-RAY DIFFRACTION98.29
1.4-1.440.12962150.10444083X-RAY DIFFRACTION97.95
1.44-1.490.11062120.1024026X-RAY DIFFRACTION96.87
1.49-1.550.11162170.10064128X-RAY DIFFRACTION98.77
1.55-1.620.12282160.10534090X-RAY DIFFRACTION98.2
1.62-1.710.13492150.11034100X-RAY DIFFRACTION98.16
1.71-1.820.1342160.11484097X-RAY DIFFRACTION97.84
1.82-1.960.13172140.11914066X-RAY DIFFRACTION97.23
1.96-2.150.13252130.12474039X-RAY DIFFRACTION96.35
2.15-2.460.14842180.13124144X-RAY DIFFRACTION98.2
2.46-3.10.18992180.14384143X-RAY DIFFRACTION97.93
3.1-41.060.1652220.1414209X-RAY DIFFRACTION97.21

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