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- PDB-6lva: Cu- Carbonic Anhydrase II pH 7.8 20 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6lva
TitleCu- 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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / COPPER (II) ION / 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)29,5525
Polymers29,2891
Non-polymers2634
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-19 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.359, 41.402, 72.307
Angle α, β, γ (deg.)90.000, 103.972, 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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 41.45 %
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: 73862 / % possible obs: 96.9 % / Redundancy: 7.5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Net I/σ(I): 25.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3600 / CC1/2: 0.906 / CC star: 0.975 / Rpim(I) all: 0.175 / Rrim(I) all: 0.481 / % possible all: 94.3

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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: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.876 / SU ML: 0.018 / 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
Rfree0.1419 3775 -
Rwork0.113 --
all0.114 --
obs-73841 96.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.042 Å2-0 Å2-0.019 Å2
2--0.106 Å20 Å2
3----0.049 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 11 360 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192220
X-RAY DIFFRACTIONr_bond_other_d0.0030.022067
X-RAY DIFFRACTIONr_angle_refined_deg2.461.9523032
X-RAY DIFFRACTIONr_angle_other_deg1.22234805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80824.904104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.522157
X-RAY DIFFRACTIONr_chiral_restr0.1830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212562
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02513
X-RAY DIFFRACTIONr_nbd_refined0.340.21682
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24018
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22088
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.390.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3260.283
X-RAY DIFFRACTIONr_nbd_other0.2820.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.25
X-RAY DIFFRACTIONr_mcbond_it2.4050.7971078
X-RAY DIFFRACTIONr_mcbond_other2.130.7931077
X-RAY DIFFRACTIONr_mcangle_it2.5061.2051361
X-RAY DIFFRACTIONr_mcangle_other2.5191.2071362
X-RAY DIFFRACTIONr_scbond_it3.5451.071142
X-RAY DIFFRACTIONr_scbond_other3.5451.071142
X-RAY DIFFRACTIONr_scangle_it3.9791.491665
X-RAY DIFFRACTIONr_scangle_other3.9781.491666
X-RAY DIFFRACTIONr_lrange_it8.6689.0932858
X-RAY DIFFRACTIONr_lrange_other5.8627.8462653
X-RAY DIFFRACTIONr_sphericity_free46.338588
X-RAY DIFFRACTIONr_sphericity_bonded14.64954488
X-RAY DIFFRACTIONr_rigid_bond_restr6.07934287
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
1.2-1.2310.2822520.2575002558994.00610.225
1.231-1.2650.2222630.1734936548894.7340.149
1.265-1.3010.1482660.1054753527795.11090.093
1.301-1.3410.1322820.0934654516995.49240.08
1.341-1.3850.1392220.094560499295.79330.078
1.385-1.4340.1432340.0854436485396.22910.075
1.434-1.4880.1212460.0814276468196.60330.073
1.488-1.5480.1222260.0814124449296.83880.074
1.548-1.6170.1232350.0843936429197.20350.079
1.617-1.6960.1261930.0853852415697.32920.081
1.696-1.7870.122080.0883624391297.9550.087
1.787-1.8950.1181800.0913495374498.15710.092
1.895-2.0250.1191670.0943287351298.34850.096
2.025-2.1870.1371600.0993068326798.80620.104
2.187-2.3940.1171490.0982814299598.93150.106
2.394-2.6750.1511280.1092604275399.23720.12
2.675-3.0840.1181040.1152292240899.50170.128
3.084-3.7680.1351320.1231938207899.6150.143
3.768-5.2870.168760.1551524161399.1940.178
5.287-30.0020.271520.27188294598.8360.317

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