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- PDB-8zwv: The Crystal Structure of carbonic anhydrase II from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8zwv
TitleThe Crystal Structure of carbonic anhydrase II from Biortus.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Metal-binding
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
methanesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of carbonic anhydrase II from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
History
DepositionJun 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 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)29,6936
Polymers29,3461
Non-polymers3475
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.525, 72.204, 74.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 29346.111 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 BL21(DE3) (bacteria)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase
#2: Chemical ChemComp-V7Z / methanesulfonamide / 72879 / Methane sulfonamide / Methylsulfonamide


Mass: 95.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M CaCl2, 0.1M Hepes pH7.5, 30% PEG4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.5→42.53 Å / Num. obs: 37316 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.999 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1847 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ONV

7onv


Resolution: 1.5→36.905 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.382 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1874 1903 5.108 %
Rwork0.1523 35352 -
all0.154 --
obs-37255 99.928 %
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: 16.999 Å2
Baniso -1Baniso -2Baniso -3
1--0.931 Å2-0 Å20 Å2
2--1.73 Å2-0 Å2
3----0.799 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 18 244 2335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162051
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.8352979
X-RAY DIFFRACTIONr_angle_other_deg0.6341.7824762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9255273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.04658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71910372
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.84510101
X-RAY DIFFRACTIONr_chiral_restr0.0960.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
X-RAY DIFFRACTIONr_nbd_refined0.2020.2368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21799
X-RAY DIFFRACTIONr_nbtor_refined0.180.21025
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2157
X-RAY DIFFRACTIONr_metal_ion_refined0.160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1110.27
X-RAY DIFFRACTIONr_nbd_other0.1560.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2440.223
X-RAY DIFFRACTIONr_mcbond_it1.5681.5761053
X-RAY DIFFRACTIONr_mcbond_other1.5611.5751053
X-RAY DIFFRACTIONr_mcangle_it2.272.8311318
X-RAY DIFFRACTIONr_mcangle_other2.282.8321319
X-RAY DIFFRACTIONr_scbond_it3.3491.9151139
X-RAY DIFFRACTIONr_scbond_other3.3481.9161140
X-RAY DIFFRACTIONr_scangle_it5.0563.321654
X-RAY DIFFRACTIONr_scangle_other5.0543.3211655
X-RAY DIFFRACTIONr_lrange_it5.95419.3942432
X-RAY DIFFRACTIONr_lrange_other5.74716.082363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2411380.2225900.22127280.9460.9561000.196
1.539-1.5810.2291430.225070.20226500.9510.9671000.179
1.581-1.6270.2231380.19124120.19325510.9540.9799.96080.168
1.627-1.6770.1911300.17423870.17525180.9710.97599.96030.15
1.677-1.7320.2021230.1722840.17124070.9650.9781000.149
1.732-1.7920.187970.15322560.15423530.9790.9831000.134
1.792-1.860.191310.1521690.15223010.9770.98599.95650.133
1.86-1.9350.1881270.1420380.14321650.9790.9871000.124
1.935-2.0210.1581140.13919910.1421050.9840.9881000.126
2.021-2.120.183920.14319250.14520170.9760.9871000.132
2.12-2.2340.1861090.14618160.14819250.9770.9861000.136
2.234-2.3690.17940.14517270.14718210.980.9871000.137
2.369-2.5320.172900.15416230.15517130.9810.9851000.148
2.532-2.7330.242770.15415250.15816030.9640.98599.93760.147
2.733-2.9930.184860.14614050.14814920.980.98699.9330.144
2.993-3.3430.159650.14212830.14313500.9840.98799.85190.146
3.343-3.8550.204550.14511610.14712180.9760.98799.83580.155
3.855-4.7090.175340.1359970.13610350.9790.98999.61350.15
4.709-6.6050.173280.1517880.1528220.990.98899.27010.167
6.605-36.9050.172320.1744680.1735060.9780.97898.81420.183

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