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- PDB-9f2e: Carbonic anhydrase II variant with bound iron complex in space gr... -

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Basic information

Entry
Database: PDB / ID: 9f2e
TitleCarbonic anhydrase II variant with bound iron complex in space group C2 (ArPase)
ComponentsCarbonic anhydrase 2
KeywordsOXIDOREDUCTASE / artifical enzyme / peroxidase / human carbonic anhydrase
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
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.015 Å
AuthorsJakob, R.P. / Ward, T.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation180544 Switzerland
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 23, 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)30,1165
Polymers29,2841
Non-polymers8324
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-37 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.392, 47.200, 71.092
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number5
Space group name H-MC121

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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: 29283.895 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
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.015→41.722 Å / Num. obs: 17306 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Net I/σ(I): 9.5
Reflection shellResolution: 2.015→2.09 Å / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1683 / CC1/2: 0.51 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2801: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.015→41.722 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 866 5 %
Rwork0.1804 --
obs0.1826 17303 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.015→41.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 48 182 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092202
X-RAY DIFFRACTIONf_angle_d1.1383014
X-RAY DIFFRACTIONf_dihedral_angle_d4.51769
X-RAY DIFFRACTIONf_chiral_restr0.059304
X-RAY DIFFRACTIONf_plane_restr0.007391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.015-2.14090.29831420.25922695X-RAY DIFFRACTION99
2.1409-2.30610.2811430.22782721X-RAY DIFFRACTION100
2.3061-2.53820.2511430.20622716X-RAY DIFFRACTION100
2.5382-2.90540.24811440.19282735X-RAY DIFFRACTION100
2.9054-3.66020.25671450.17762755X-RAY DIFFRACTION100
3.6602-41.7220.16931490.14852815X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2037-0.2875-0.04710.42940.18250.18130.0160.16820.36760.04030.01160.0991-0.2027-0.07120.00040.3081-0.00330.02010.27540.00250.307717.949735.5793-6.1959
20.2412-0.00030.37420.4947-0.02650.52580.05420.13530.0462-0.30380.0531-0.20830.1736-0.0010.00110.3559-0.00840.06710.2595-0.0090.317532.747620.8894-15.5432
30.9725-0.12860.12651.3612-0.23480.8393-0.0360.156-0.0461-0.32490.09470.00430.1283-0.017700.2527-0.0241-0.00770.2385-0.01170.193424.86222.3707-15.8923
40.3216-0.3170.17150.3143-0.07610.36080.08510.28040.44120.00770.04070.1467-0.2945-0.1288-0.00020.3271-0.0171-0.01660.29020.02710.311323.143634.9383-16.3646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 237 )
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 259 )

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