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- PDB-6nj5: Thermostable variant of human carbonic anhydrase II with disorder... -

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Basic information

Entry
Database: PDB / ID: 6nj5
TitleThermostable variant of human carbonic anhydrase II with disordered tetrazine 2.0 at site 233
ComponentsCarbonic anhydrase 2
KeywordsLYASE / genetic code expansion / thermostability / protein engineering
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / 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 / 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKean, K.M. / Karplus, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF MCB-1518265 United States
CitationJournal: ACS Appl Mater Interfaces / Year: 2019
Title: Immobilization of Proteins with Controlled Load and Orientation.
Authors: Bednar, R.M. / Golbek, T.W. / Kean, K.M. / Brown, W.J. / Jana, S. / Baio, J.E. / Karplus, P.A. / Mehl, R.A.
History
DepositionJan 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 28, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,3072
Polymers30,2421
Non-polymers651
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.419, 72.460, 151.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 30241.906 Da / Num. of mol.: 1 / Mutation: A64T, L99H, K153N, L223S, L239P, A247T
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
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 362 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M SODIUM CHLORIDE, 0.1 M TRIS PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→37.88 Å / Num. obs: 55819 / % possible obs: 82 % / Redundancy: 10.2 % / CC1/2: 1 / Net I/σ(I): 6.6
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 483 / CC1/2: 0.27 / % possible all: 68

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIX(1.12_2829)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CA2

1ca2


Resolution: 1.25→37.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.83
RfactorNum. reflection% reflection
Rfree0.206 2776 4.99 %
Rwork0.166 --
obs0.168 55671 81.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 1 362 2492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082399
X-RAY DIFFRACTIONf_angle_d1.0083305
X-RAY DIFFRACTIONf_dihedral_angle_d15.712918
X-RAY DIFFRACTIONf_chiral_restr0.084342
X-RAY DIFFRACTIONf_plane_restr0.008435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.27160.36621110.34662106X-RAY DIFFRACTION67
1.2716-1.29470.36421180.3272499X-RAY DIFFRACTION77
1.2947-1.31960.32591310.29432509X-RAY DIFFRACTION79
1.3196-1.34650.34291200.26392498X-RAY DIFFRACTION78
1.3465-1.37580.30741050.25842504X-RAY DIFFRACTION78
1.3758-1.40780.2911160.23342500X-RAY DIFFRACTION78
1.4078-1.4430.25311100.21862469X-RAY DIFFRACTION77
1.443-1.4820.23121540.21032419X-RAY DIFFRACTION76
1.482-1.52560.25091590.20362416X-RAY DIFFRACTION76
1.5256-1.57490.24321430.18492388X-RAY DIFFRACTION75
1.5749-1.63120.20321480.16722371X-RAY DIFFRACTION75
1.6312-1.69650.18741330.17382398X-RAY DIFFRACTION74
1.6965-1.77370.20241030.17512453X-RAY DIFFRACTION75
1.7737-1.86720.19671210.17452578X-RAY DIFFRACTION80
1.8672-1.98420.2061240.18322814X-RAY DIFFRACTION87
1.9842-2.13740.19951650.16563015X-RAY DIFFRACTION92
2.1374-2.35240.21951630.16083161X-RAY DIFFRACTION97
2.3524-2.69280.20412190.15863128X-RAY DIFFRACTION98
2.6928-3.39230.18931670.14243258X-RAY DIFFRACTION98
3.3923-37.89430.16831660.13543411X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 12.6822 Å / Origin y: 13.382 Å / Origin z: -18.7652 Å
111213212223313233
T0.0876 Å20.0027 Å20.0011 Å2-0.0954 Å2-0.0119 Å2--0.074 Å2
L1.1275 °20.3911 °2-0.0213 °2-1.4538 °2-0.0581 °2--0.8356 °2
S-0.0205 Å °0.0887 Å °0.0042 Å °-0.0991 Å °0.0173 Å °-0.0027 Å °-0.0097 Å °-0.0275 Å °-0.0025 Å °
Refinement TLS groupSelection details: CHAIN A

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