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- PDB-4cnx: Surface residue engineering of bovine carbonic anhydrase to an ex... -

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Basic information

Entry
Database: PDB / ID: 4cnx
TitleSurface residue engineering of bovine carbonic anhydrase to an extreme halophilic enzyme for potential application in postcombustion CO2 capture
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / PROTEIN ENGINEERING / CO2 CAPTURE
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase activity / cyanamide hydratase / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / apical part of cell ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase activity / cyanamide hydratase / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / apical part of cell / zinc ion binding / plasma membrane / 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
DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 2
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsWarden, A. / Newman, J. / Peat, T.S. / Seabrook, S. / Williams, M. / Dojchinov, G. / Haritos, V.
CitationJournal: Nat.Commun. / Year: 2015
Title: Rational Engineering of a Mesohalophilic Carbonic Anhydrase to an Extreme Halotolerant Biocatalyst.
Authors: Warden, A.C. / Williams, M. / Peat, T.S. / Seabrook, S.A. / Newman, J. / Dojchinov, G. / Haritos, V.S.
History
DepositionJan 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5983
Polymers29,4261
Non-polymers1722
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.591, 67.937, 43.134
Angle α, β, γ (deg.)90.00, 103.07, 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 II / CA-II


Mass: 29426.455 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P00921, 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 5.5
Details: PROTEIN WAS AT 10 MG/ML. THE RESERVOIR CONDITIONS WERE: 40% PEG 600, 100 MM SODIUM CITRATE AT PH 5.5 SET UP AT 8C. CROSS SEEDING FROM OTHER MUTANT CA-II CRYSTALS WAS USED TO OBTAIN THESE CRYSTALS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.23→42 Å / Num. obs: 66095 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.7
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6.2 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ML2

3ml2


Resolution: 1.23→35.76 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.035 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THERE IS 'EXTRA' ELECTRON DENSITY NEAR ASP129 WHICH MAKES IT LOOK LIKE THIS MIGHT BE GLUTAMIC ACID INSTEAD OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THERE IS 'EXTRA' ELECTRON DENSITY NEAR ASP129 WHICH MAKES IT LOOK LIKE THIS MIGHT BE GLUTAMIC ACID INSTEAD OF ASPARTIC ACID, BUT THE PLASMID SEQUENCE WAS CHECKED AND THE PROTEIN WAS CHECKED BY MASS SPEC AND BOTH SUGGEST THAT THE RESIDUE SHOULD BE ASP.
RfactorNum. reflection% reflectionSelection details
Rfree0.14683 3344 5.1 %RANDOM
Rwork0.11065 ---
obs0.11244 62737 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.268 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.11 Å2
2---0.11 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.23→35.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 8 405 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192318
X-RAY DIFFRACTIONr_bond_other_d0.0010.022071
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.9553189
X-RAY DIFFRACTIONr_angle_other_deg0.96834831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51825.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57615365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9811510
X-RAY DIFFRACTIONr_chiral_restr0.140.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212765
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02523
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_it1.571.0841135
X-RAY DIFFRACTIONr_mcbond_other1.5681.0841134
X-RAY DIFFRACTIONr_mcangle_it2.0641.8531452
X-RAY DIFFRACTIONr_mcangle_other2.0661.8541453
X-RAY DIFFRACTIONr_scbond_it4.7081.5061183
X-RAY DIFFRACTIONr_scbond_other4.7051.5061183
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7372.3771738
X-RAY DIFFRACTIONr_long_range_B_refined4.6027.9843085
X-RAY DIFFRACTIONr_long_range_B_other4.6017.9853086
X-RAY DIFFRACTIONr_rigid_bond_restr5.72234389
X-RAY DIFFRACTIONr_sphericity_free32.997565
X-RAY DIFFRACTIONr_sphericity_bonded10.69154647
LS refinement shellResolution: 1.235→1.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 229 -
Rwork0.183 4369 -
obs--92.81 %

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