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- PDB-9f15: Carbonic anhydrase II variant with bound iron complex -

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Basic information

Entry
Database: PDB / ID: 9f15
TitleCarbonic anhydrase II variant with bound iron complex
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Artificial Matalloenzymes / Carbonic Anhydrase II
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 / 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 / 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
: / ACETATE ION / methanesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhang, K. / Jakob, R.P. / Ward, T.R.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Catalysis / Year: 2024
Title: Directed Evolution of an Artificial Hydroxylase Based on a Thermostable Human Carbonic Anhydrase Protein
Authors: Morita, I. / Faraone, A. / Salvisberg, E. / Zhang, K. / Jakob, R.P. / Maier, T. / Ward, T.R.
History
DepositionApr 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 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)30,3036
Polymers29,3781
Non-polymers9245
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-27 kcal/mol
Surface area11800 Å2
Unit cell
Length a, b, c (Å)46.344, 70.664, 146.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29378.098 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 BL21(DE3) (bacteria)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-A1H9O / 4,4,7,10,10-pentamethyl-3,6,8,11-tetrakis(oxidanylidene)-N-[2-(4-sulfamoylphenyl)ethyl]-2,5,7,9,12-pentazabicyclo[11.4.0]heptadeca-1(13),14,16-triene-15-carboxamide containing iron


Mass: 639.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29FeN7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-V7Z / methanesulfonamide / 72879 / Methane sulfonamide / Methylsulfonamide


Mass: 95.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Na Acet, 0.1 M Na Cacod 6.5 pH, 30 %w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.93→38.75 Å / Num. obs: 17297 / % possible obs: 93.41 % / Redundancy: 13.1 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.045 / Rrim(I) all: 0.166 / Net I/σ(I): 12.29
Reflection shellResolution: 1.93→1.999 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.303 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 1563 / CC1/2: 0.711 / CC star: 0.912 / Rpim(I) all: 0.376 / Rrim(I) all: 1.358 / % possible all: 85.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→38.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.581 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24122 858 5 %RANDOM
Rwork0.18051 ---
obs0.18354 16439 93.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.93→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 53 104 2213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122175
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161962
X-RAY DIFFRACTIONr_angle_refined_deg1.811.8662970
X-RAY DIFFRACTIONr_angle_other_deg0.5871.7874548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4355256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.3759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32610353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it2.4992.6011028
X-RAY DIFFRACTIONr_mcbond_other2.4922.61027
X-RAY DIFFRACTIONr_mcangle_it3.3414.6611282
X-RAY DIFFRACTIONr_mcangle_other3.3394.6631283
X-RAY DIFFRACTIONr_scbond_it3.3542.951147
X-RAY DIFFRACTIONr_scbond_other3.3442.9481143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9935.2621686
X-RAY DIFFRACTIONr_long_range_B_refined6.06825.742395
X-RAY DIFFRACTIONr_long_range_B_other6.08125.482336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 50 -
Rwork0.246 1029 -
obs--80.88 %

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