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- PDB-5bru: Catalytic Improvement of an Artificial Metalloenzyme by Computati... -

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Basic information

Entry
Database: PDB / ID: 5bru
TitleCatalytic Improvement of an Artificial Metalloenzyme by Computational Design
ComponentsCarbonic anhydrase 2
KeywordsOXIDOREDUCTASE / artificial metalloenzyme
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-8TH / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsHeinisch, T. / Pellizzoni, M. / Duerrenberger, M. / Tinberg, C.E. / Koehler, V. / Klehr, J. / Haeussinger, D. / Baker, D. / Ward, T.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design.
Authors: Heinisch, T. / Pellizzoni, M. / Durrenberger, M. / Tinberg, C.E. / Kohler, V. / Klehr, J. / Haussinger, D. / Baker, D. / Ward, T.R.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,3435
Polymers29,2921
Non-polymers1,0514
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.308, 41.689, 72.343
Angle α, β, γ (deg.)90.00, 104.26, 90.00
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


Mass: 29292.125 Da / Num. of mol.: 1 / Mutation: L140M, L197M, C205S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8TH / chloro[(phenylsulfonyl){[4-(4-sulfamoylphenyl)pyridin-2-yl-kappaN]methyl}azanide-kappaN][(1,2,3,4,5-eta)-1,2,3,4-tetramethyl-5-propylcyclopentadienyl]iridium


Mass: 793.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H35ClIrN3O4S2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 2.6 M ammonium sulfate, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3051 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3051 Å / Relative weight: 1
ReflectionResolution: 1.6→70.11 Å / Num. obs: 29218 / % possible obs: 90.3 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.048 / Net I/σ(I): 11.6 / Num. measured all: 137882
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.6-1.633.80.7192.133038770.4820.40155.4
8.76-70.114.70.05225.710542230.9960.02699

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å41 Å
Translation1.6 Å41 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimless0.5.1data scaling
PHASER2.5.7phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZP9

3zp9


Resolution: 1.6→70.11 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.661 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19358 1542 5.3 %RANDOM
Rwork0.13717 ---
obs0.14008 27665 89.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.57 Å2
2---0.57 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 52 173 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192185
X-RAY DIFFRACTIONr_bond_other_d0.0030.021991
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.983004
X-RAY DIFFRACTIONr_angle_other_deg1.00434613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02224.59298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.221157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212431
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02492
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_it2.0921.5011036
X-RAY DIFFRACTIONr_mcbond_other2.0351.4971035
X-RAY DIFFRACTIONr_mcangle_it2.2332.2461295
X-RAY DIFFRACTIONr_mcangle_other2.2322.251296
X-RAY DIFFRACTIONr_scbond_it2.9881.9221149
X-RAY DIFFRACTIONr_scbond_other2.5621.8441092
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7962.6231591
X-RAY DIFFRACTIONr_long_range_B_refined3.74814.0862589
X-RAY DIFFRACTIONr_long_range_B_other3.08912.7912413
X-RAY DIFFRACTIONr_rigid_bond_restr3.01234176
X-RAY DIFFRACTIONr_sphericity_free18.156557
X-RAY DIFFRACTIONr_sphericity_bonded6.80954224
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 75 -
Rwork0.325 1273 -
obs--56.14 %

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