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- PDB-6lv8: Ni- Carbonic Anhydrase II pH 11.0 20 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6lv8
TitleNi- Carbonic Anhydrase II pH 11.0 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 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 / 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 / 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)29,6046
Polymers29,2891
Non-polymers3155
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.419, 41.398, 72.191
Angle α, β, γ (deg.)90.000, 104.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 351 molecules

#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11 / 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: 73282 / % possible obs: 96.1 % / Redundancy: 7.5 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 40.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 10.1 / Num. unique obs: 3542 / CC1/2: 0.975 / CC star: 0.994 / Rpim(I) all: 0.09 / Rrim(I) all: 0.244 / % possible all: 93

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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: 0.776 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.032
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1364 3748 -
Rwork0.1121 --
all0.113 --
obs-73217 96.09 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.121 Å2-0 Å2-0.024 Å2
2--0.019 Å2-0 Å2
3---0.101 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 15 346 2410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192223
X-RAY DIFFRACTIONr_bond_other_d0.0030.022067
X-RAY DIFFRACTIONr_angle_refined_deg2.3521.9533035
X-RAY DIFFRACTIONr_angle_other_deg1.24734805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88624.904104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54415372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.356157
X-RAY DIFFRACTIONr_chiral_restr0.1940.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212566
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02513
X-RAY DIFFRACTIONr_nbd_refined0.290.21676
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.23972
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22104
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3080.298
X-RAY DIFFRACTIONr_nbd_other0.30.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.24
X-RAY DIFFRACTIONr_mcbond_it3.0640.811078
X-RAY DIFFRACTIONr_mcbond_other2.0330.8051077
X-RAY DIFFRACTIONr_mcangle_it3.5211.2231361
X-RAY DIFFRACTIONr_mcangle_other3.5461.2261362
X-RAY DIFFRACTIONr_scbond_it2.8661.0531145
X-RAY DIFFRACTIONr_scbond_other2.8691.0531142
X-RAY DIFFRACTIONr_scangle_it3.8521.4741668
X-RAY DIFFRACTIONr_scangle_other3.8541.4751666
X-RAY DIFFRACTIONr_lrange_it4.7178.7952851
X-RAY DIFFRACTIONr_lrange_other3.9817.7922663
X-RAY DIFFRACTIONr_sphericity_free50.339573
X-RAY DIFFRACTIONr_sphericity_bonded12.29954493
X-RAY DIFFRACTIONr_rigid_bond_restr6.08434290
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
1.2-1.2310.2482530.1874971559493.38580.157
1.231-1.2650.1682640.134871548093.70440.112
1.265-1.3010.1382630.0974683525594.11990.085
1.301-1.3410.1292810.0834631518994.66180.073
1.341-1.3850.1232140.0794505497394.89240.069
1.385-1.4340.1222370.084391484695.50140.072
1.434-1.4880.122400.0794253468995.820.072
1.488-1.5480.1162220.0774083448496.0080.072
1.548-1.6170.1132400.0813889428796.31440.077
1.617-1.6960.1091890.0853837417496.45420.083
1.696-1.7870.1292040.0943595389897.46020.094
1.787-1.8950.1181770.0963470373597.64390.098
1.895-2.0250.1151680.13259351697.46870.105
2.025-2.1870.1291600.1013056326598.49920.108
2.187-2.3940.1221510.1032796299698.36450.114
2.394-2.6750.1531250.1212584274298.79650.136
2.675-3.0840.1521040.1272284241299.0050.145
3.084-3.7680.1161310.1271923206899.3230.152
3.768-5.2870.174710.1571499161797.09340.185
5.287-30.0020.249520.27286994697.35730.325

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