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- PDB-6luw: Zn- Carbonic Anhydrase II pH 7.8 0 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6luw
TitleZn- 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 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 / positive regulation of synaptic transmission, GABAergic / 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 / 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
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)29,4473
Polymers29,2891
Non-polymers1582
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.206, 41.283, 72.147
Angle α, β, γ (deg.)90.000, 104.184, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 263 / 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: 40.88 %
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: 74586 / % possible obs: 98.8 % / Redundancy: 7.3 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 29.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 3646 / CC1/2: 0.938 / CC star: 0.984 / Rpim(I) all: 0.151 / Rrim(I) all: 0.106 / % possible all: 97.5

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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: 0.974 / SU B: 0.848 / SU ML: 0.018 / 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
Rfree0.1409 3820 -
Rwork0.1165 --
all0.118 --
obs-74561 98.768 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.109 Å2
Baniso -1Baniso -2Baniso -3
1--0.112 Å2-0 Å2-0.025 Å2
2--0.089 Å20 Å2
3---0.032 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 7 263 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192227
X-RAY DIFFRACTIONr_bond_other_d0.0020.022071
X-RAY DIFFRACTIONr_angle_refined_deg2.4371.9513044
X-RAY DIFFRACTIONr_angle_other_deg1.23334813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52224.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.037157
X-RAY DIFFRACTIONr_chiral_restr0.1920.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02515
X-RAY DIFFRACTIONr_nbd_refined0.2720.21418
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23976
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22078
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2122
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3120.277
X-RAY DIFFRACTIONr_nbd_other0.3010.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.24
X-RAY DIFFRACTIONr_mcbond_it2.1870.981084
X-RAY DIFFRACTIONr_mcbond_other2.1490.9751083
X-RAY DIFFRACTIONr_mcangle_it2.8281.481371
X-RAY DIFFRACTIONr_mcangle_other2.8721.4831372
X-RAY DIFFRACTIONr_scbond_it3.7141.3011143
X-RAY DIFFRACTIONr_scbond_other3.7141.3011143
X-RAY DIFFRACTIONr_scangle_it4.4631.8161669
X-RAY DIFFRACTIONr_scangle_other4.4621.8161670
X-RAY DIFFRACTIONr_lrange_it4.9089.5662712
X-RAY DIFFRACTIONr_lrange_other4.6179.0032597
X-RAY DIFFRACTIONr_sphericity_free44.357558
X-RAY DIFFRACTIONr_sphericity_bonded12.63254430
X-RAY DIFFRACTIONr_rigid_bond_restr5.90134298
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
1.2-1.2310.2312550.2285135553397.41550.195
1.231-1.2650.2052660.1614976537897.47120.136
1.265-1.3010.1382930.1064847526697.60730.09
1.301-1.3410.132770.0914746512697.99060.079
1.341-1.3850.1252290.0824630494798.22110.071
1.385-1.4340.1362320.0844474478098.45190.074
1.434-1.4880.1222480.084328463498.74840.072
1.488-1.5480.1152230.0774182445498.89990.072
1.548-1.6170.1232430.0813985426799.0860.077
1.617-1.6960.121920.0823884410899.2210.079
1.696-1.7870.1232150.0893672390099.66670.089
1.787-1.8950.1171790.0963504369499.70220.098
1.895-2.0250.1331650.1043290346299.79780.109
2.025-2.1870.1311650.106309132561000.113
2.187-2.3940.1181510.106281529661000.117
2.394-2.6750.161270.124257727041000.14
2.675-3.0840.1441050.1322302240899.95850.154
3.084-3.7680.1411270.1321912204199.9020.158
3.768-5.2870.177740.1581514161098.63350.196
5.287-30.0020.202520.25286893298.71240.308

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