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- PDB-6km4: Human Carbonic Anhydrase II native 07 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6km4
TitleHuman Carbonic Anhydrase II native 07 atm CO2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / intermediate states / water network / point mutation
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
CARBON DIOXIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2019R1A2C1004274 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Structural insights into the effect of active-site mutation on the catalytic mechanism of carbonic anhydrase.
Authors: Kim, J.K. / Lee, C. / Lim, S.W. / Andring, J.T. / Adhikari, A. / McKenna, R. / Kim, C.U.
History
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 3, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Nov 22, 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)29,5355
Polymers29,2891
Non-polymers2464
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-31 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 41.317, 72.225
Angle α, β, γ (deg.)90.000, 104.036, 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
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


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


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


Mass: 18.015 Da / Num. of mol.: 364 / 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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 9, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. obs: 84284 / % possible obs: 97.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.01
Reflection shellResolution: 1.15→1.17 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5.53 / Num. unique obs: 4103

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Processing

Software
NameVersionClassification
REFMAC5.8.0124 2015/06/02refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUK

5yuk


Resolution: 1.15→29.074 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.697 / SU ML: 0.015 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1242 4090 -
Rwork0.098 --
all0.099 --
obs-84072 97.902 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.005 Å2-0 Å2-0 Å2
2--0.007 Å2-0 Å2
3----0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.15→29.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 13 364 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192327
X-RAY DIFFRACTIONr_bond_other_d0.0030.022173
X-RAY DIFFRACTIONr_angle_refined_deg2.3681.9533185
X-RAY DIFFRACTIONr_angle_other_deg1.24535069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31424.862109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25115402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.798158
X-RAY DIFFRACTIONr_chiral_restr0.1590.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212723
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02541
X-RAY DIFFRACTIONr_nbd_refined0.3010.21720
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.24190
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22156
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2980.2113
X-RAY DIFFRACTIONr_nbd_other0.3240.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.213
X-RAY DIFFRACTIONr_mcbond_it1.7471.0511127
X-RAY DIFFRACTIONr_mcbond_other1.6911.0481126
X-RAY DIFFRACTIONr_mcangle_it2.3551.5941439
X-RAY DIFFRACTIONr_mcangle_other2.3881.5961440
X-RAY DIFFRACTIONr_scbond_it3.9271.3861200
X-RAY DIFFRACTIONr_scbond_other3.9271.3861200
X-RAY DIFFRACTIONr_scangle_it4.7861.9291738
X-RAY DIFFRACTIONr_scangle_other4.7851.9291739
X-RAY DIFFRACTIONr_lrange_it4.97911.0082964
X-RAY DIFFRACTIONr_lrange_other4.449.942770
X-RAY DIFFRACTIONr_sphericity_free44.438578
X-RAY DIFFRACTIONr_sphericity_bonded12.45154703
X-RAY DIFFRACTIONr_rigid_bond_restr6.7434500
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
1.15-1.180.1592740.1375865635896.55550.114
1.18-1.2120.1442790.1155634611596.69660.094
1.212-1.2470.1162550.15552597897.13950.082
1.247-1.2850.1232730.0895366579897.25770.073
1.285-1.3280.1092410.0835260563497.63930.069
1.328-1.3740.1172630.0795057544997.63260.067
1.374-1.4260.1052580.0744901526498.00530.064
1.426-1.4840.1052580.0694725507698.16780.062
1.484-1.550.1062480.0684538485498.59910.064
1.55-1.6250.0962740.0684316464798.77340.066
1.625-1.7130.11990.0724171441099.0930.072
1.713-1.8160.1221970.0813984421499.21690.085
1.816-1.9410.1281950.0843723393999.46690.093
1.941-2.0960.1131970.0863478369499.48570.1
2.096-2.2950.1241760.0923217340499.67690.111
2.295-2.5630.1281640.1082903308199.54560.133
2.563-2.9560.1321370.1152588273599.63440.146
2.956-3.6110.116820.1172221230599.91320.154
3.611-5.0680.154850.1181726181899.6150.159
5.068-29.0740.197350.187736107271.92160.261

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