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- PDB-6lv5: Ni- Carbonic Anhydrase II pH 7.8 0 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6lv5
TitleNi- 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 / METAL BINDING PROTEIN-LYASE complex
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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
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
NICKEL (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)29,4994
Polymers29,2891
Non-polymers2093
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-20 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.399, 41.285, 71.917
Angle α, β, γ (deg.)90.000, 104.027, 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


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


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 41.01 %
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: 73023 / % possible obs: 96.6 % / Redundancy: 7.5 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.034 / Rrim(I) all: 0.093 / Net I/σ(I): 20.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 7.6 / Num. unique obs: 3517 / CC1/2: 0.942 / CC star: 0.985 / Rpim(I) all: 0.131 / Rrim(I) all: 0.356 / % possible all: 93.8

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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: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.828 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.033 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.141 3734 -
Rwork0.1163 --
all0.118 --
obs-73007 96.568 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.027 Å20 Å2-0.06 Å2
2---0.033 Å2-0 Å2
3---0.081 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 8 279 2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0192231
X-RAY DIFFRACTIONr_bond_other_d0.0040.022075
X-RAY DIFFRACTIONr_angle_refined_deg2.61.9523051
X-RAY DIFFRACTIONr_angle_other_deg1.3434825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55525106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46915374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.794157
X-RAY DIFFRACTIONr_chiral_restr0.1980.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212584
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02515
X-RAY DIFFRACTIONr_nbd_refined0.2810.21484
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.24040
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22074
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0020.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2720.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.286
X-RAY DIFFRACTIONr_nbd_other0.3430.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.26
X-RAY DIFFRACTIONr_mcbond_it1.7720.8481083
X-RAY DIFFRACTIONr_mcbond_other1.7080.8421082
X-RAY DIFFRACTIONr_mcangle_it2.3421.2781369
X-RAY DIFFRACTIONr_mcangle_other2.371.2821370
X-RAY DIFFRACTIONr_scbond_it3.2131.1521148
X-RAY DIFFRACTIONr_scbond_other3.2131.1521148
X-RAY DIFFRACTIONr_scangle_it3.6211.6011676
X-RAY DIFFRACTIONr_scangle_other3.621.6021677
X-RAY DIFFRACTIONr_lrange_it4.8248.6772741
X-RAY DIFFRACTIONr_lrange_other4.1758.0192609
X-RAY DIFFRACTIONr_sphericity_free35.176557
X-RAY DIFFRACTIONr_sphericity_bonded12.6354455
X-RAY DIFFRACTIONr_rigid_bond_restr6.71534306
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
1.2-1.2310.2042510.1954940554593.61590.175
1.231-1.2650.22610.1524822538494.40940.137
1.265-1.3020.1342760.0984736529094.74480.091
1.302-1.3420.1422700.0934603512195.15720.087
1.342-1.3860.1422250.0874524496595.64950.082
1.386-1.4340.132270.0844357477196.08050.08
1.434-1.4880.1282380.0854233464596.2540.083
1.488-1.5490.1122220.0814079445196.630.081
1.549-1.6170.1212390.0883888426796.7190.09
1.617-1.6960.1341860.093824413896.90670.094
1.696-1.7880.1312040.0953608389397.91930.101
1.788-1.8960.121790.0973451369898.16120.105
1.896-2.0260.121610.13249348597.84790.111
2.026-2.1870.1151600.1023038323598.85630.118
2.187-2.3950.1161510.1062790298198.65820.126
2.395-2.6750.171250.1212560271299.00440.147
2.675-3.0850.1311040.1322276239399.45670.165
3.085-3.7690.1381310.131920205999.61150.169
3.769-5.2880.185720.1611507160598.38010.216
5.288-30.0020.246520.27686893698.29060.363

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