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- PDB-8wer: Carbonic Anhydrase II T200V variant 0 atm CO2 pressure (pH 7.8) -

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Basic information

Entry
Database: PDB / ID: 8wer
TitleCarbonic Anhydrase II T200V variant 0 atm CO2 pressure (pH 7.8)
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Carbonic Anhydrase / enzyme mechanism / metalloenzymes
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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateSSTF-BA1702-04 (Samsung Science and Technology Foundation) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2025
Title: Fast product release requires active-site water dynamics in carbonic anhydrase.
Authors: Kim, J.K. / Lim, S.W. / Jeong, H. / Lee, C. / Kim, S. / Son, D.W. / Kumar, R. / Andring, J.T. / Lomelino, C. / Wierman, J.L. / Cohen, A.E. / Shin, T.J. / Ghim, C.M. / McKenna, R. / Jo, B.H. ...Authors: Kim, J.K. / Lim, S.W. / Jeong, H. / Lee, C. / Kim, S. / Son, D.W. / Kumar, R. / Andring, J.T. / Lomelino, C. / Wierman, J.L. / Cohen, A.E. / Shin, T.J. / Ghim, C.M. / McKenna, R. / Jo, B.H. / Min, D. / Choi, J.M. / Kim, C.U.
History
DepositionSep 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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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)29,3522
Polymers29,2871
Non-polymers651
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.107, 41.292, 72.312
Angle α, β, γ (deg.)90.00, 104.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2


Mass: 29287.090 Da / Num. of mol.: 1 / Mutation: T200V
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3M sodium citrate, 50mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6D / Wavelength: 0.97934 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Mar 22, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 44044 / % possible obs: 96.3 % / Redundancy: 7.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.025 / Rrim(I) all: 0.069 / Net I/σ(I): 30.9
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2102 / CC1/2: 0.79 / CC star: 0.939 / Rpim(I) all: 0.268 / Rrim(I) all: 0.657 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.1 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15539 2170 4.9 %RANDOM
Rwork0.11555 ---
obs0.11761 41828 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.03 Å2
2---0.36 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.42→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 1 292 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192222
X-RAY DIFFRACTIONr_bond_other_d0.0030.022068
X-RAY DIFFRACTIONr_angle_refined_deg2.4421.9463037
X-RAY DIFFRACTIONr_angle_other_deg1.23934805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95324.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.045157
X-RAY DIFFRACTIONr_chiral_restr0.180.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212572
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02515
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5511.4431084
X-RAY DIFFRACTIONr_mcbond_other2.551.4371083
X-RAY DIFFRACTIONr_mcangle_it3.2132.1711371
X-RAY DIFFRACTIONr_mcangle_other3.2142.1751372
X-RAY DIFFRACTIONr_scbond_it5.0461.7881138
X-RAY DIFFRACTIONr_scbond_other5.0751.7891138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6452.5351662
X-RAY DIFFRACTIONr_long_range_B_refined8.65513.4782735
X-RAY DIFFRACTIONr_long_range_B_other5.61212.692595
X-RAY DIFFRACTIONr_rigid_bond_restr4.86734290
X-RAY DIFFRACTIONr_sphericity_free34.347567
X-RAY DIFFRACTIONr_sphericity_bonded15.84154441
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 129 -
Rwork0.205 2950 -
obs--92.6 %

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