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- PDB-6nj2: thermostable carbonic anhydrase II variant with tetrazine 2.0 at ... -

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Basic information

Entry
Database: PDB / ID: 6nj2
Titlethermostable carbonic anhydrase II variant with tetrazine 2.0 at site 186
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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / 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: 1.5 Å
AuthorsKean, K.M. / Karplus, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)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 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 28, 2020Group: Database references / Derived calculations / Category: citation_author / struct_conn / struct_conn_type
Item: _citation_author.identifier_ORCID / _struct_conn.conn_type_id ..._citation_author.identifier_ORCID / _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_asym_id / _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_asym_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 1.4Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0839
Polymers60,4842
Non-polymers5997
Water10,431579
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4954
Polymers30,2421
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5885
Polymers30,2421
Non-polymers3464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 93.680, 101.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M AMMONIUM SULFATE, 30% PEG 4000, 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: Apr 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→36.04 Å / Num. obs: 94004 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 8.72
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 6873 / CC1/2: 0.2 / Rrim(I) all: 435.5 / % possible all: 100

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Processing

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

1ca2


Resolution: 1.5→37.25 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 9160 5.07 %
Rwork0.172 --
obs0.173 180549 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 30 579 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0314377
X-RAY DIFFRACTIONf_angle_d1.0315959
X-RAY DIFFRACTIONf_dihedral_angle_d13.1632573
X-RAY DIFFRACTIONf_chiral_restr0.062619
X-RAY DIFFRACTIONf_plane_restr0.007775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.40973340.40465657X-RAY DIFFRACTION100
1.5171-1.53490.39413070.36975726X-RAY DIFFRACTION100
1.5349-1.55360.34953120.34035674X-RAY DIFFRACTION100
1.5536-1.57330.32323220.32715708X-RAY DIFFRACTION100
1.5733-1.5940.34312970.31855696X-RAY DIFFRACTION100
1.594-1.61580.3012890.30815761X-RAY DIFFRACTION100
1.6158-1.63890.30843250.29765685X-RAY DIFFRACTION100
1.6389-1.66340.3063190.28995738X-RAY DIFFRACTION100
1.6634-1.68940.28753400.2775603X-RAY DIFFRACTION100
1.6894-1.71710.28442920.265792X-RAY DIFFRACTION100
1.7171-1.74670.26642800.25345716X-RAY DIFFRACTION100
1.7467-1.77840.24073010.23685699X-RAY DIFFRACTION100
1.7784-1.81260.24683110.23395750X-RAY DIFFRACTION100
1.8126-1.84960.24813030.21815677X-RAY DIFFRACTION100
1.8496-1.88990.23433280.20835702X-RAY DIFFRACTION100
1.8899-1.93380.21492990.19445733X-RAY DIFFRACTION100
1.9338-1.98220.1662680.16745769X-RAY DIFFRACTION100
1.9822-2.03580.17123010.15985712X-RAY DIFFRACTION100
2.0358-2.09570.17983550.14775623X-RAY DIFFRACTION100
2.0957-2.16330.17073110.1485685X-RAY DIFFRACTION100
2.1633-2.24060.16332820.13875775X-RAY DIFFRACTION100
2.2406-2.33030.15823160.13615692X-RAY DIFFRACTION100
2.3303-2.43630.14983060.12895741X-RAY DIFFRACTION100
2.4363-2.56480.15073310.12695716X-RAY DIFFRACTION100
2.5648-2.72540.15873280.13095621X-RAY DIFFRACTION100
2.7254-2.93580.15872780.12875794X-RAY DIFFRACTION100
2.9358-3.2310.173010.13615723X-RAY DIFFRACTION100
3.231-3.69820.16543170.13125703X-RAY DIFFRACTION100
3.6982-4.65790.1652400.12025764X-RAY DIFFRACTION100
4.6579-37.26110.16262670.16815754X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72770.0652-0.05750.7415-0.29141.0830.0155-0.01020.01460.05320.0216-0.0064-0.0358-0.01390.00150.12180.00150.01520.1108-0.00040.1323-7.7821-14.056924.2894
20.7031-0.17230.1861.0339-0.20510.81560.0125-0.007-0.01160.0063-0.01270.0220.0399-0.0109-0.00020.11440.00610.00140.1349-0.00280.115722.5641-0.877541.4222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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