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- PDB-3zp9: Human Carbonic Anhydrase II as a Scaffold for an Artificial Trans... -

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Basic information

Entry
Database: PDB / ID: 3zp9
TitleHuman Carbonic Anhydrase II as a Scaffold for an Artificial Transfer Hydrogenase
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / ARTIFICIAL METALLOENZYME / INHIBITOR / IRIDIUM PENTAMETHYLCYCLOPENTADIENYL / PIANO STOOL COMPLEX
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 / angiotensin-activated signaling pathway / regulation of chloride transport / Reversible hydration of carbon dioxide ...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 / angiotensin-activated signaling pathway / regulation of chloride transport / Reversible hydration of carbon dioxide / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / 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-9TH / MERCURIBENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsHeinisch, T. / Schirmer, T.
CitationJournal: Chem.Sci. / Year: 2013
Title: Human Carbonic Anhydrase II as Host Protein for the Creation of Artificial Metalloenzymes: The Asymmetric Transfer Hydrogenation of Imines
Authors: Monnard, F.W. / Nogueira, E.S. / Heinisch, T. / Schirmer, T. / Ward, T.R.
History
DepositionFeb 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Structure summary
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details ..._exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct.title

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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)30,6266
Polymers29,2891
Non-polymers1,3375
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.500, 41.620, 72.480
Angle α, β, γ (deg.)90.00, 103.80, 90.00
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: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 172 molecules

#2: Chemical ChemComp-9TH / pentamethylcyclopentadienyl iridium [N-benzensulfonamide-(2-pyridylmethyl-4-benzensulfonamide)amin] chloride


Mass: 765.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31ClIrN3O4S2
#3: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.2 Å3/Da / Density % sol: 42.7 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 2.1 M AMSO4, 50 MM TRIS-SO4, 0.2 MM 4-CHLOROMERCURIBENZOIC ACID, 4 MG/ML PROTEIN, PH 7.9, 293 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→40.01 Å / Num. obs: 49267 / % possible obs: 82.9 % / Observed criterion σ(I): 1.25 / Redundancy: 3.2 % / Biso Wilson estimate: 13.08 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 1.31→1.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 1.26 / % possible all: 43.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PYK

3pyk


Resolution: 1.31→40.011 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1932 2019 4.1 %
Rwork0.1683 --
obs0.1693 49213 82.89 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.91 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2071 Å20 Å20.9784 Å2
2--2.1497 Å20 Å2
3----1.9426 Å2
Refinement stepCycle: LAST / Resolution: 1.31→40.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 62 167 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182214
X-RAY DIFFRACTIONf_angle_d1.792978
X-RAY DIFFRACTIONf_dihedral_angle_d15.357788
X-RAY DIFFRACTIONf_chiral_restr0.117301
X-RAY DIFFRACTIONf_plane_restr0.01384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.34280.3318590.30351443X-RAY DIFFRACTION36
1.3428-1.37910.2982710.29791941X-RAY DIFFRACTION48
1.3791-1.41970.35811090.31732435X-RAY DIFFRACTION61
1.4197-1.46550.30191440.26173404X-RAY DIFFRACTION84
1.4655-1.51790.27631670.23823627X-RAY DIFFRACTION90
1.5179-1.57870.22431570.19233694X-RAY DIFFRACTION91
1.5787-1.65050.23641610.18023734X-RAY DIFFRACTION92
1.6505-1.73750.2191640.16123787X-RAY DIFFRACTION94
1.7375-1.84640.18251530.14883812X-RAY DIFFRACTION94
1.8464-1.9890.18721610.14873725X-RAY DIFFRACTION91
1.989-2.18910.18341750.14323844X-RAY DIFFRACTION94
2.1891-2.50580.18891600.15383802X-RAY DIFFRACTION93
2.5058-3.15690.16681680.15073921X-RAY DIFFRACTION96
3.1569-40.030.16691700.16394025X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 11.9742 Å / Origin y: -2.2676 Å / Origin z: 15.9867 Å
111213212223313233
T0.0757 Å2-0.0056 Å2-0.0005 Å2-0.0756 Å20.0031 Å2--0.0811 Å2
L0.8841 °2-0.1482 °2-0.093 °2-0.7696 °2-0.0154 °2--0.8618 °2
S0.001 Å °-0.0026 Å °0.0447 Å °-0.0356 Å °0.0197 Å °-0.0181 Å °-0.0153 Å °0.0152 Å °-0.0145 Å °
Refinement TLS groupSelection details: CHAIN A

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