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- PDB-8vzg: Carbonic anhydrase II mutant with DRD function -

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Basic information

Entry
Database: PDB / ID: 8vzg
TitleCarbonic anhydrase II mutant with DRD function
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Destabilized domain / acetazolamide binding mutant / CA2
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 / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / one-carbon metabolic process / 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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / CITRATE ANION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSethi, D.K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Functional regulation of membrane-bound cytokine activity in engineered T cells via drug-responsive domains derived from carbonic anhydrase 2
Authors: Innis, M. / Meulen, J.T. / Sethi, D.K.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: 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)30,1358
Polymers29,3161
Non-polymers8187
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-59 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.534, 69.042, 80.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29316.086 Da / Num. of mol.: 1 / Mutation: S56N
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

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Non-polymers , 5 types, 213 molecules

#2: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.45M sodium citrate, 0.1M Tris-HCl pH 8.0, 4% v/v Polypropylene glycol P 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.79→29.15 Å / Num. obs: 22756 / % possible obs: 99.1 % / Redundancy: 11.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.029 / Rrim(I) all: 0.099 / Χ2: 0.96 / Net I/σ(I): 18.3 / Num. measured all: 266549
Reflection shellResolution: 1.79→1.83 Å / % possible obs: 88.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.729 / Num. measured all: 8169 / Num. unique obs: 1169 / CC1/2: 0.796 / Rpim(I) all: 0.283 / Rrim(I) all: 0.786 / Χ2: 0.87 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→29.15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.288 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 1126 4.959 %RANDOM
Rwork0.1501 21580 --
all0.152 ---
obs-22706 99.118 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.041 Å20 Å2-0 Å2
2---0.013 Å20 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 46 206 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122196
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162019
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.832987
X-RAY DIFFRACTIONr_angle_other_deg0.5841.7824682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9785265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.9859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09210356
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.5721099
X-RAY DIFFRACTIONr_chiral_restr0.0850.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022564
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02490
X-RAY DIFFRACTIONr_nbd_refined0.1980.2360
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21847
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21025
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2160
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.211
X-RAY DIFFRACTIONr_nbd_other0.1810.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.216
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0460.22
X-RAY DIFFRACTIONr_mcbond_it2.1482.1851051
X-RAY DIFFRACTIONr_mcbond_other2.1462.1841051
X-RAY DIFFRACTIONr_mcangle_it3.1353.9021319
X-RAY DIFFRACTIONr_mcangle_other3.1343.9061320
X-RAY DIFFRACTIONr_scbond_it3.2352.4921145
X-RAY DIFFRACTIONr_scbond_other3.2352.4941146
X-RAY DIFFRACTIONr_scangle_it4.9214.3871668
X-RAY DIFFRACTIONr_scangle_other4.924.3881669
X-RAY DIFFRACTIONr_lrange_it6.64424.5212396
X-RAY DIFFRACTIONr_lrange_other6.4623.972355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.8360.237960.2151415X-RAY DIFFRACTION90.6963
1.836-1.8860.252720.1871505X-RAY DIFFRACTION97.8895
1.886-1.9410.224780.171502X-RAY DIFFRACTION100
1.941-20.212560.1541468X-RAY DIFFRACTION100
2-2.0660.184750.1381414X-RAY DIFFRACTION100
2.066-2.1380.21610.1391369X-RAY DIFFRACTION100
2.138-2.2180.181670.1431325X-RAY DIFFRACTION100
2.218-2.3080.184760.1441261X-RAY DIFFRACTION100
2.308-2.410.166690.1541222X-RAY DIFFRACTION100
2.41-2.5270.2600.1491184X-RAY DIFFRACTION100
2.527-2.6620.169630.1491124X-RAY DIFFRACTION100
2.662-2.8220.158590.1481040X-RAY DIFFRACTION100
2.822-3.0150.239490.1591030X-RAY DIFFRACTION100
3.015-3.2540.225590.149929X-RAY DIFFRACTION100
3.254-3.560.126470.142853X-RAY DIFFRACTION100
3.56-3.9730.143540.136776X-RAY DIFFRACTION100
3.973-4.5730.151380.132724X-RAY DIFFRACTION100
4.573-5.5670.175120.135624X-RAY DIFFRACTION100
5.567-7.7330.223240.184492X-RAY DIFFRACTION100
7.733-29.150.184110.166323X-RAY DIFFRACTION100

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