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- PDB-8wes: Carbonic Anhydrase II T200V variant 5 atm CO2 pressure (pH 7.8) -

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Basic information

Entry
Database: PDB / ID: 8wes
TitleCarbonic Anhydrase II T200V variant 5 atm CO2 pressure (pH 7.8)
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Carbonic Anhydrase / enzyme mechanism / metalloenzymes
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
BICARBONATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateSSTF-BA1702-04 (Samsung Science and Technology Foundation) Korea, Republic Of
CitationJournal: To Be Published
Title: Temperature series of human Carbonic Anhydrase II with photolysis of caged CO2
Authors: Kim, C.U. / Kim, J.K.
History
DepositionSep 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 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)29,4143
Polymers29,2871
Non-polymers1262
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-38 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.005, 41.477, 72.303
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2


Mass: 29287.090 Da / Num. of mol.: 1 / Mutation: T200V
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3M sodium citrate, 50mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6D / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Mar 22, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 41806 / % possible obs: 97.2 % / Redundancy: 7.1 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.031 / Rrim(I) all: 0.085 / Net I/σ(I): 26
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2031 / CC1/2: 0.826 / CC star: 0.951 / Rpim(I) all: 0.246 / Rrim(I) all: 0.537 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.117 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15782 2028 4.9 %RANDOM
Rwork0.12014 ---
obs0.12204 39688 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.572 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0.14 Å2
2---0.57 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 5 282 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0192237
X-RAY DIFFRACTIONr_bond_other_d0.0030.022081
X-RAY DIFFRACTIONr_angle_refined_deg2.6051.9473057
X-RAY DIFFRACTIONr_angle_other_deg1.26634834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69824.811106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.55158
X-RAY DIFFRACTIONr_chiral_restr0.1720.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212595
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8731.41089
X-RAY DIFFRACTIONr_mcbond_other2.7361.3951088
X-RAY DIFFRACTIONr_mcangle_it3.3442.1081379
X-RAY DIFFRACTIONr_mcangle_other3.3442.1121380
X-RAY DIFFRACTIONr_scbond_it4.9691.7291148
X-RAY DIFFRACTIONr_scbond_other4.9681.7291145
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4512.4451671
X-RAY DIFFRACTIONr_long_range_B_refined6.56612.8982739
X-RAY DIFFRACTIONr_long_range_B_other5.44612.222607
X-RAY DIFFRACTIONr_rigid_bond_restr5.24234318
X-RAY DIFFRACTIONr_sphericity_free43.508564
X-RAY DIFFRACTIONr_sphericity_bonded15.72654462
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 137 -
Rwork0.217 2787 -
obs--91.83 %

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