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- PDB-7y2g: Zn-Carbonic Anhydrase II complexed with 3NPA after UV at 160 K -

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Basic information

Entry
Database: PDB / ID: 7y2g
TitleZn-Carbonic Anhydrase II complexed with 3NPA after UV at 160 K
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 / CARBON DIOXIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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
DepositionJun 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: 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)29,4594
Polymers29,2891
Non-polymers1703
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-23 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.302, 41.412, 72.260
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli (E. coli) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 160 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6D / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 2, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 72818 / % possible obs: 95.9 % / Redundancy: 3.8 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Net I/σ(I): 27.1
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3471 / CC1/2: 0.884 / CC star: 0.969 / Rpim(I) all: 0.191 / Rrim(I) all: 0.351 / % possible all: 91

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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
Starting model: 6LUW

6luw


Resolution: 1.2→29.13 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.972 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.033 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14857 3582 4.9 %RANDOM
Rwork0.11946 ---
obs0.12084 69220 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.2→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 8 243 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192222
X-RAY DIFFRACTIONr_bond_other_d0.0030.022059
X-RAY DIFFRACTIONr_angle_refined_deg2.3881.9483028
X-RAY DIFFRACTIONr_angle_other_deg1.1934784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73524.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20615371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.416157
X-RAY DIFFRACTIONr_chiral_restr0.1660.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212562
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02513
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_it3.0861.1181079
X-RAY DIFFRACTIONr_mcbond_other2.4491.111078
X-RAY DIFFRACTIONr_mcangle_it3.5071.6861363
X-RAY DIFFRACTIONr_mcangle_other3.5421.691364
X-RAY DIFFRACTIONr_scbond_it5.0771.4951143
X-RAY DIFFRACTIONr_scbond_other5.0971.4961138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1612.0831657
X-RAY DIFFRACTIONr_long_range_B_refined6.87610.6622649
X-RAY DIFFRACTIONr_long_range_B_other5.49110.1472546
X-RAY DIFFRACTIONr_rigid_bond_restr5.78234281
X-RAY DIFFRACTIONr_sphericity_free58.146575
X-RAY DIFFRACTIONr_sphericity_bonded14.20154375
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 240 -
Rwork0.167 4853 -
obs--91.13 %

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