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- PDB-6qfw: Human carbonic anhydrase II with bound IrCp* complex (cofactor 9)... -

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Basic information

Entry
Database: PDB / ID: 6qfw
TitleHuman carbonic anhydrase II with bound IrCp* complex (cofactor 9) to generate an artificial transfer hydrogenase (ATHase)
ComponentsCarbonic anhydrase 2
KeywordsOXIDOREDUCTASE / Artificial Transfer Hydrogenase / bound IrCp* complex / zinc binding protein / human 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 / 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, 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
: / Chem-JR8 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsRebelein, J.G.
Funding support Switzerland, Germany, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_162348 Switzerland
European Research CouncilDrEAM
Swiss National Science FoundationNCCR MSE Switzerland
European Molecular Biology OrganizationALTF 194-2017 Germany
CitationJournal: Acs Catalysis / Year: 2019
Title: Chemical Optimization of Whole-Cell Transfer Hydrogenation Using Carbonic Anhydrase as Host Protein.
Authors: Rebelein, J.G. / Cotelle, Y. / Garabedian, B. / Ward, T.R.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)30,3245
Polymers29,2731
Non-polymers1,0514
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-19 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.232, 41.441, 72.374
Angle α, β, γ (deg.)90.000, 104.360, 90.000
Int Tables number4
Space group name H-MP1211

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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


Mass: 29273.062 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 (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 271 molecules

#2: Chemical ChemComp-JR8 / 4-[3-(8-chloranyl-2',3',4',5',6'-pentamethyl-4-oxidanyl-7-oxidanylidene-spiro[1$l^{4},8$l^{4}-diaza-9$l^{7}-iridabicyclo[4.3.0]nona-1,3,5-triene-9,1'-1$l^{7}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane]-8-yl)propyl]benzenesulfonamide


Mass: 697.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H31ClIrN3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ir
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 2.6 M ammonium sulfate, 50 mM Tris-H2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→40.95 Å / Num. obs: 70789 / % possible obs: 98 % / Redundancy: 9.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.5
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7 / Num. unique obs: 5020 / CC1/2: 0.975 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZP9

3zp9


Resolution: 1.2→40.95 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1784 3708 5 %RANDOM
Rwork0.1622 ---
obs0.163 70789 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.48 Å2 / Biso mean: 14.7 Å2 / Biso min: 5.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.1 Å2
2---0.06 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.2→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 42 268 2349
Biso mean--73.51 26.36 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132254
X-RAY DIFFRACTIONr_bond_other_d0.0340.0172010
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.7843122
X-RAY DIFFRACTIONr_angle_other_deg2.3711.5844720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14423.964111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89215373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.397157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022523
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02447
X-RAY DIFFRACTIONr_mcbond_it1.4561.2631065
X-RAY DIFFRACTIONr_mcbond_other1.4531.2621064
X-RAY DIFFRACTIONr_mcangle_it2.1291.9041339
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 260 -
Rwork0.205 5020 -
all-5280 -
obs--94.35 %

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