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- PDB-6lux: Zn- Carbonic Anhydrase II pH 7.8 20 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6lux
TitleZn- Carbonic Anhydrase II pH 7.8 20 atm CO2
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / LYASE / metalloenzymes / carbonic anhydrase / enzyme mechanism / metal coordination geometry / proton transfer / biological water dynamics
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
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
National Research Foundation (NRF, Korea)2019R1A2C1004274 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2020
Title: Elucidating the role of metal ions in carbonic anhydrase catalysis.
Authors: Kim, J.K. / Lee, C. / Lim, S.W. / Adhikari, A. / Andring, J.T. / McKenna, R. / Ghim, C.M. / Kim, C.U.
History
DepositionFeb 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5355
Polymers29,2891
Non-polymers2464
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-31 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.369, 41.442, 72.133
Angle α, β, γ (deg.)90.000, 104.049, 90.000
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.: 2 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 17, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 73208 / % possible obs: 96.2 % / Redundancy: 7.4 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Net I/σ(I): 29.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3522 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.263 / Rrim(I) all: 0.72 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124 2015/06/02refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0124phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUK

5yuk


Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.964 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1418 3748 -
Rwork0.1128 --
all0.114 --
obs-73183 96.118 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.193 Å2
Baniso -1Baniso -2Baniso -3
1--0.032 Å2-0 Å2-0.065 Å2
2--0.059 Å2-0 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 13 367 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192225
X-RAY DIFFRACTIONr_bond_other_d0.0030.022068
X-RAY DIFFRACTIONr_angle_refined_deg2.4231.9523037
X-RAY DIFFRACTIONr_angle_other_deg1.20934807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68224.904104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.139157
X-RAY DIFFRACTIONr_chiral_restr0.1940.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212569
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02514
X-RAY DIFFRACTIONr_nbd_refined0.3030.21694
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24024
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22102
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22092
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2144
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.22
X-RAY DIFFRACTIONr_metal_ion_refined0.070.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3120.2101
X-RAY DIFFRACTIONr_nbd_other0.2310.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.27
X-RAY DIFFRACTIONr_mcbond_it3.3791.051081
X-RAY DIFFRACTIONr_mcbond_other3.1811.0471080
X-RAY DIFFRACTIONr_mcangle_it4.5041.5881366
X-RAY DIFFRACTIONr_mcangle_other4.5141.591367
X-RAY DIFFRACTIONr_scbond_it3.2811.331144
X-RAY DIFFRACTIONr_scbond_other3.2811.331144
X-RAY DIFFRACTIONr_scangle_it4.0141.8731666
X-RAY DIFFRACTIONr_scangle_other4.0131.8731667
X-RAY DIFFRACTIONr_lrange_it6.28911.0672872
X-RAY DIFFRACTIONr_lrange_other5.5839.9062674
X-RAY DIFFRACTIONr_sphericity_free44.123586
X-RAY DIFFRACTIONr_sphericity_bonded13.44354503
X-RAY DIFFRACTIONr_rigid_bond_restr6.07934293
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.2-1.2310.322520.2884951561892.6130.257
1.231-1.2650.2362650.2114857545993.82670.184
1.265-1.3010.172630.1374703527294.19580.118
1.301-1.3410.1482830.114610517094.64220.092
1.341-1.3850.1522140.0974527498395.14350.082
1.385-1.4340.1362340.0884380483295.48840.073
1.434-1.4880.1382390.0844237467595.74330.071
1.488-1.5480.1162260.084098449696.17440.069
1.548-1.6170.1142390.0783873426896.34490.07
1.617-1.6960.1251880.0823833416996.450.075
1.696-1.7870.1232060.0853590389497.48330.08
1.787-1.8950.1161770.0873477373897.75280.085
1.895-2.0250.1231650.0923258351097.52140.092
2.025-2.1870.1221590.0953052325898.55740.097
2.187-2.3940.1141510.0942799299898.39890.099
2.394-2.6750.1391250.1032582273998.83170.11
2.675-3.0840.1271040.112281240699.12720.122
3.084-3.7680.1311310.1141927206999.46830.134
3.768-5.2870.159750.1431518161498.69890.166
5.287-30.0020.274520.26487794498.4110.309

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