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- PDB-9u5b: T200H Carbonic Anhydrase II pH 7.8 5 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 9u5b
TitleT200H Carbonic Anhydrase II pH 7.8 5 atm CO2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Metal Binding Protein
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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / 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 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsLim, S.W. / Kim, C.U.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2022R1A2C2091815 Korea, Republic Of
CitationJournal: Mol.Cells / Year: 2025
Title: Conformational flexibility of His200 enables catalytic activity in the T200H mutant of carbonic anhydrase II.
Authors: Lim, S.W. / Jeong, H. / Kim, G.H. / Min, D. / Kim, J.K. / Kim, C.U.
History
DepositionMar 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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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)30,2813
Polymers30,1551
Non-polymers1262
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.161, 41.401, 72.682
Angle α, β, γ (deg.)90.000, 104.622, 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 / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 30154.977 Da / Num. of mol.: 1 / Mutation: T200H
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, cyanamide hydratase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#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
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3M of Sodium Citrate 50mM Tris-HCl pH 7.8

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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: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 67198 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 1.017 / Net I/σ(I): 22.37
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3270 / CC1/2: 0.809 / CC star: 0.946 / Rpim(I) all: 0.293 / Rrim(I) all: 0.591 / Χ2: 0.484 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.058 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.144 / SU B: 1.399 / SU ML: 0.027 / Average fsc free: 0.9805 / Average fsc work: 0.9868 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.042
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1704 3427 5.101 %
Rwork0.1432 63756 -
all0.145 --
obs-67183 99.822 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.024 Å20 Å20.063 Å2
2---0.122 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 5 263 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162019
X-RAY DIFFRACTIONr_angle_refined_deg1.9111.8172995
X-RAY DIFFRACTIONr_angle_other_deg0.6861.7834694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.52557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24810365
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.44510103
X-RAY DIFFRACTIONr_chiral_restr0.1070.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022605
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02496
X-RAY DIFFRACTIONr_nbd_refined0.2040.2411
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21882
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21036
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2159
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.213
X-RAY DIFFRACTIONr_nbd_other0.240.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_mcbond_it3.7971.1831065
X-RAY DIFFRACTIONr_mcbond_other3.7491.1831065
X-RAY DIFFRACTIONr_mcangle_it5.3642.131342
X-RAY DIFFRACTIONr_mcangle_other5.3742.1321343
X-RAY DIFFRACTIONr_scbond_it5.2471.4051129
X-RAY DIFFRACTIONr_scbond_other5.2311.4091127
X-RAY DIFFRACTIONr_scangle_it7.6052.4461649
X-RAY DIFFRACTIONr_scangle_other7.5882.451647
X-RAY DIFFRACTIONr_lrange_it10.5514.3942480
X-RAY DIFFRACTIONr_lrange_other9.98913.182418
X-RAY DIFFRACTIONr_rigid_bond_restr4.04734213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.25-1.2820.2572150.2446120.24149210.9650.9798.08980.227
1.282-1.3170.2282320.20445750.20548080.9710.97899.97920.187
1.317-1.3560.1992260.17644540.17746800.9740.9821000.159
1.356-1.3970.1742340.14843430.14945780.980.98699.97820.129
1.397-1.4430.1842460.13541590.13744060.980.98899.97730.116
1.443-1.4930.1792640.12439860.12742620.980.9999.71840.106
1.493-1.550.1522360.11439100.11641460.9870.9921000.1
1.55-1.6130.1621720.11137990.11339710.9840.9921000.097
1.613-1.6840.1291880.10636100.10737980.9890.9931000.094
1.684-1.7660.151680.1134610.11236290.9850.9931000.101
1.766-1.8610.1692000.11732820.1234830.9830.99299.97130.112
1.861-1.9740.1631630.12631590.12833220.9830.9911000.122
1.974-2.1090.1661620.13429210.13630830.9850.991000.134
2.109-2.2770.1651270.13527450.13628720.9830.9891000.138
2.277-2.4930.1741220.13925460.14126680.9830.9881000.146
2.493-2.7850.1451530.14822680.14824210.9860.9861000.157
2.785-3.2110.209890.16420550.16621440.970.9831000.185
3.211-3.920.1541130.15117100.15218260.9860.98699.83570.178
3.92-5.4940.185690.1513610.15214300.9840.991000.184
5.494-29.0580.18480.1937990.1928470.9840.9811000.228

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