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- PDB-6nj3: Thermostable variant of human carbonic anhydrase with ordered tet... -

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Basic information

Entry
Database: PDB / ID: 6nj3
TitleThermostable variant of human carbonic anhydrase with ordered 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 / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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
ACETATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 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_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 1.4Oct 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3663
Polymers30,2421
Non-polymers1242
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.144, 69.083, 81.106
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.: 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 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: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.01→40.56 Å / Num. obs: 115504 / % possible obs: 97.6 % / Redundancy: 10.66 % / Net I/σ(I): 27.28
Reflection shellResolution: 1.01→1.04 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1987 / CC1/2: 0.39 / Rrim(I) all: 135.1 / % possible all: 86.6

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Processing

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

1ca2


Resolution: 1.01→40.55 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.125 5763 4.99 %
Rwork0.1 --
obs0.102 115429 88.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.01→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 5 443 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112428
X-RAY DIFFRACTIONf_angle_d0.9553342
X-RAY DIFFRACTIONf_dihedral_angle_d18.576929
X-RAY DIFFRACTIONf_chiral_restr0.079345
X-RAY DIFFRACTIONf_plane_restr0.007453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0105-1.02190.3505220.5238399X-RAY DIFFRACTION10
1.0219-1.0340.3216520.36371140X-RAY DIFFRACTION28
1.034-1.04660.2933910.28251675X-RAY DIFFRACTION41
1.0466-1.05980.26411240.24732202X-RAY DIFFRACTION54
1.0598-1.07380.1991420.21752716X-RAY DIFFRACTION67
1.0738-1.08850.19951660.19313220X-RAY DIFFRACTION79
1.0885-1.1040.1881920.1613529X-RAY DIFFRACTION87
1.104-1.12050.1652070.13473869X-RAY DIFFRACTION95
1.1205-1.1380.13932120.12253974X-RAY DIFFRACTION98
1.138-1.15670.13592250.10964064X-RAY DIFFRACTION99
1.1567-1.17660.12692120.10564061X-RAY DIFFRACTION100
1.1766-1.1980.12392180.09834083X-RAY DIFFRACTION100
1.198-1.22110.11861910.09374113X-RAY DIFFRACTION100
1.2211-1.2460.13172340.09544088X-RAY DIFFRACTION100
1.246-1.27310.10982300.09534074X-RAY DIFFRACTION100
1.2731-1.30270.12282050.0914135X-RAY DIFFRACTION100
1.3027-1.33530.11272160.08864104X-RAY DIFFRACTION100
1.3353-1.37140.10361910.08914129X-RAY DIFFRACTION100
1.3714-1.41170.11392080.08834111X-RAY DIFFRACTION100
1.4117-1.45730.10062170.08764107X-RAY DIFFRACTION100
1.4573-1.50940.11362280.08754100X-RAY DIFFRACTION100
1.5094-1.56980.1152000.08584171X-RAY DIFFRACTION100
1.5698-1.64130.11312090.08834135X-RAY DIFFRACTION100
1.6413-1.72780.11692210.08934123X-RAY DIFFRACTION100
1.7278-1.83610.11772510.09344133X-RAY DIFFRACTION100
1.8361-1.97780.11532130.08994166X-RAY DIFFRACTION100
1.9778-2.17690.11582380.08714147X-RAY DIFFRACTION100
2.1769-2.49180.11612250.09254204X-RAY DIFFRACTION100
2.4918-3.13920.1142010.09844271X-RAY DIFFRACTION100
3.1392-40.58570.13842220.10584423X-RAY DIFFRACTION100

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