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- PDB-6km0: Human Carbonic Anhydrase II V143I variant 07 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6km0
TitleHuman Carbonic Anhydrase II V143I variant 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
BICARBONATE ION / CARBON DIOXIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5665
Polymers29,3031
Non-polymers2634
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-28 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.300, 41.496, 72.144
Angle α, β, γ (deg.)90.000, 104.225, 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: 29303.090 Da / Num. of mol.: 1 / Mutation: V143I
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, 359 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 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: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 0.93→50 Å / Num. obs: 152384 / % possible obs: 93.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.44
Reflection shellResolution: 0.93→0.95 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 6283

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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: 3U7C

3u7c


Resolution: 0.93→29.166 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.406 / SU ML: 0.01 / Cross valid method: FREE R-VALUE / ESU R: 0.016 / ESU R Free: 0.016
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1219 7455 -
Rwork0.1077 --
all0.108 --
obs-152358 93.725 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å20 Å20.002 Å2
2--0.002 Å2-0 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 0.93→29.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 14 355 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192402
X-RAY DIFFRACTIONr_bond_other_d0.0030.022254
X-RAY DIFFRACTIONr_angle_refined_deg2.5821.9573294
X-RAY DIFFRACTIONr_angle_other_deg1.40135264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43124.955111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65615422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.489158
X-RAY DIFFRACTIONr_chiral_restr0.1710.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212832
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02556
X-RAY DIFFRACTIONr_nbd_refined0.3230.21850
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.24158
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22132
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3740.2110
X-RAY DIFFRACTIONr_nbd_other0.3030.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.212
X-RAY DIFFRACTIONr_mcbond_it1.9970.9041164
X-RAY DIFFRACTIONr_mcbond_other1.5450.9011163
X-RAY DIFFRACTIONr_mcangle_it2.4031.371494
X-RAY DIFFRACTIONr_mcangle_other2.4061.3711495
X-RAY DIFFRACTIONr_scbond_it2.6411.1291238
X-RAY DIFFRACTIONr_scbond_other2.641.1281233
X-RAY DIFFRACTIONr_scangle_it3.2911.5991792
X-RAY DIFFRACTIONr_scangle_other3.2871.5991789
X-RAY DIFFRACTIONr_lrange_it4.9039.2383067
X-RAY DIFFRACTIONr_lrange_other4.2098.3152838
X-RAY DIFFRACTIONr_sphericity_free53.415562
X-RAY DIFFRACTIONr_sphericity_bonded11.23654874
X-RAY DIFFRACTIONr_rigid_bond_restr6.4334656
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
0.93-0.9540.2234450.20388151199077.2310.175
0.954-0.980.1714700.18192191163283.29610.151
0.98-1.0090.1694970.1595831135688.76360.123
1.009-1.040.1435070.12497621104492.98260.101
1.04-1.0740.1224700.10595211062993.99760.087
1.074-1.1110.1084760.0993001034994.46320.077
1.111-1.1530.14820.0818985995795.07880.072
1.153-1.20.0944410.0778760959895.86370.07
1.2-1.2530.0934470.0738479925396.4660.067
1.253-1.3150.0943930.0738141880696.91120.069
1.315-1.3850.1023950.0767805839897.64230.072
1.385-1.4690.1064280.0797316792497.72840.077
1.469-1.5710.113160.0797056750698.21480.079
1.571-1.6960.1043610.086508695598.76350.084
1.696-1.8570.1093350.0916022641099.17320.099
1.857-2.0750.1352550.1035529582099.38140.112
2.075-2.3940.1192790.1114845514599.59180.118
2.394-2.9280.142190.1314152437699.88570.144
2.928-4.1190.1211580.1283253341899.79520.151
4.119-29.1660.166810.171851197198.02130.21

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