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- PDB-6lv9: Cu- Carbonic Anhydrase II pH 7.8 0 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6lv9
TitleCu- Carbonic Anhydrase II pH 7.8 0 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 / arylesterase activity / regulation of chloride transport / 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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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
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)29,5084
Polymers29,2891
Non-polymers2193
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-20 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.326, 41.225, 72.085
Angle α, β, γ (deg.)90.000, 104.169, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 40.92 %
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: 71865 / % possible obs: 95.1 % / Redundancy: 7.7 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.039 / Rrim(I) all: 0.106 / Net I/σ(I): 19.5
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 6 / Num. unique obs: 3481 / CC1/2: 0.915 / CC star: 0.977 / Rpim(I) all: 0.167 / Rrim(I) all: 0.46 / % possible all: 92.3

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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: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.881 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.033 / ESU R Free: 0.034
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1443 3689 -
Rwork0.1172 --
all0.119 --
obs-71843 95.076 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.083 Å2
2---0.017 Å2-0 Å2
3---0.208 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 8 286 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0192231
X-RAY DIFFRACTIONr_bond_other_d0.0030.022075
X-RAY DIFFRACTIONr_angle_refined_deg2.551.9523051
X-RAY DIFFRACTIONr_angle_other_deg1.28534825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4825106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5915374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.105157
X-RAY DIFFRACTIONr_chiral_restr0.2050.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212584
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02515
X-RAY DIFFRACTIONr_nbd_refined0.2820.21504
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.24040
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22074
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.22154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.310.282
X-RAY DIFFRACTIONr_nbd_other0.3060.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2440.24
X-RAY DIFFRACTIONr_mcbond_it2.370.9441083
X-RAY DIFFRACTIONr_mcbond_other2.2590.941082
X-RAY DIFFRACTIONr_mcangle_it2.7471.4251369
X-RAY DIFFRACTIONr_mcangle_other2.7691.4281370
X-RAY DIFFRACTIONr_scbond_it3.5461.2311148
X-RAY DIFFRACTIONr_scbond_other3.5451.2311148
X-RAY DIFFRACTIONr_scangle_it4.231.7271676
X-RAY DIFFRACTIONr_scangle_other4.2291.7281677
X-RAY DIFFRACTIONr_lrange_it6.4829.5162767
X-RAY DIFFRACTIONr_lrange_other6.3488.8432632
X-RAY DIFFRACTIONr_sphericity_free34.538561
X-RAY DIFFRACTIONr_sphericity_bonded14.16354458
X-RAY DIFFRACTIONr_rigid_bond_restr6.25834306
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
1.2-1.2310.2522480.2314884556492.23580.208
1.231-1.2650.2132600.1694710538192.3620.151
1.265-1.3010.1492680.1114610526092.73760.103
1.301-1.3410.1422670.0974522513093.35280.088
1.341-1.3850.1372230.0894432495993.86970.082
1.385-1.4340.1362250.0864269476794.27310.08
1.434-1.4880.1332380.0834140463394.4960.08
1.488-1.5480.1222130.0824029446595.00560.08
1.548-1.6170.1272400.0863815426195.16550.086
1.617-1.6960.1331810.0893776413095.81110.091
1.696-1.7870.1332080.0923549389396.50650.097
1.787-1.8950.1221690.0963390369596.31940.104
1.895-2.0250.1351590.1033205347896.72230.115
2.025-2.1870.1311630.1043017324498.02710.118
2.187-2.3940.1171500.1052740296997.33920.125
2.394-2.6750.161230.1182537271498.01030.143
2.675-3.0840.131020.1262267240398.58510.158
3.084-3.7680.131290.1271893204398.97210.163
3.768-5.2870.182710.1571504161097.82610.208
5.287-30.0020.244520.26485593497.10920.351

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