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- PDB-6nj6: Thermostable variant of human carbonic anhydrase with tetrazine 2... -

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Basic information

Entry
Database: PDB / ID: 6nj6
TitleThermostable variant of human carbonic anhydrase with tetrazine 2.0 at site 186 reacted with sTCO in crystallo
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 / 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
METHANOL / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.1Oct 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)61,61916
Polymers60,4842
Non-polymers1,13614
Water11,349630
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8088
Polymers30,2421
Non-polymers5667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8128
Polymers30,2421
Non-polymers5707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.330, 93.860, 100.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 644 molecules

#2: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4O
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
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: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→65.33 Å / Num. obs: 82090 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 1 / Net I/σ(I): 15.2
Reflection shellResolution: 1.6→1.63 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4002 / CC1/2: 0.32 / % possible all: 100

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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: 1.6→54.76 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2
RfactorNum. reflection% reflection
Rfree0.193 4139 5.05 %
Rwork0.164 --
obs0.165 82005 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→54.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 61 630 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194548
X-RAY DIFFRACTIONf_angle_d1.0526209
X-RAY DIFFRACTIONf_dihedral_angle_d12.5822694
X-RAY DIFFRACTIONf_chiral_restr0.064643
X-RAY DIFFRACTIONf_plane_restr0.007808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.38811440.37342566X-RAY DIFFRACTION100
1.6182-1.63720.36791460.35882549X-RAY DIFFRACTION100
1.6372-1.65720.32521200.33352551X-RAY DIFFRACTION100
1.6572-1.67820.30961640.30362560X-RAY DIFFRACTION100
1.6782-1.70030.26741430.28292541X-RAY DIFFRACTION100
1.7003-1.72360.29111290.26872569X-RAY DIFFRACTION100
1.7236-1.74820.26911300.25762570X-RAY DIFFRACTION100
1.7482-1.77430.28251480.23492580X-RAY DIFFRACTION100
1.7743-1.8020.22171250.20632557X-RAY DIFFRACTION100
1.802-1.83150.23561380.20162575X-RAY DIFFRACTION100
1.8315-1.86310.23481270.19842582X-RAY DIFFRACTION100
1.8631-1.8970.21281580.18932550X-RAY DIFFRACTION100
1.897-1.93350.24071410.20862582X-RAY DIFFRACTION100
1.9335-1.9730.22141200.18472600X-RAY DIFFRACTION100
1.973-2.01590.17831280.17362556X-RAY DIFFRACTION100
2.0159-2.06280.21871290.15252614X-RAY DIFFRACTION100
2.0628-2.11430.21931500.15672583X-RAY DIFFRACTION100
2.1143-2.17150.16951590.15272561X-RAY DIFFRACTION100
2.1715-2.23540.18411420.14112568X-RAY DIFFRACTION100
2.2354-2.30760.17591170.14252600X-RAY DIFFRACTION100
2.3076-2.390.16561450.13332603X-RAY DIFFRACTION100
2.39-2.48570.15761390.13972594X-RAY DIFFRACTION100
2.4857-2.59890.1781590.13542591X-RAY DIFFRACTION100
2.5989-2.73590.16121550.13922581X-RAY DIFFRACTION100
2.7359-2.90730.16551180.13932630X-RAY DIFFRACTION100
2.9073-3.13170.1781540.1492611X-RAY DIFFRACTION100
3.1317-3.44690.20231240.14192670X-RAY DIFFRACTION100
3.4469-3.94550.16671390.13062645X-RAY DIFFRACTION100
3.9455-4.97040.15221160.12542716X-RAY DIFFRACTION100
4.9704-54.78660.19361320.20332811X-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)
10.95540.0643-0.12351.3201-0.31192.2354-0.0415-0.05080.02490.1233-0.0101-0.01280.04960.0377-0.00410.16090.01690.01610.1786-0.00840.209-9.3624-13.997123.919
21.0181-0.19750.49582.0071-0.53492.1180.07920.0441-0.0735-0.0675-0.05570.02740.25570.06510.00180.20640.03080.01110.2066-0.00610.1834-40.4032-0.39140.9346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND NOT ELEMENT ZN
2X-RAY DIFFRACTION2CHAIN B AND NOT ELEMENT ZN

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