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- PDB-7onm: Carbonic anhydrase II mutant (N67G-E69R-I91C) dually binding an I... -

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Basic information

Entry
Database: PDB / ID: 7onm
TitleCarbonic anhydrase II mutant (N67G-E69R-I91C) dually binding an IrCp* complex to generate an artificial transfer hydrogenase (ATHase)
ComponentsCarbonic anhydrase 2
KeywordsOXIDOREDUCTASE / artificial metalloenzyme / artificial transfer hydrogenase / metal binding protein
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
Chem-VKZ / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.769 Å
AuthorsStein, A. / Dongping, C. / Cotelle, Y. / Rebelein, J.G. / Ward, T.R.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_182046 Switzerland
European Molecular Biology Organization (EMBO)ALTF 194-2017European Union
CitationJournal: Acs Cent.Sci. / Year: 2021
Title: A Dual Anchoring Strategy for the Directed Evolution of Improved Artificial Transfer Hydrogenases Based on Carbonic Anhydrase.
Authors: Stein, A. / Chen, D. / Igareta, N.V. / Cotelle, Y. / Rebelein, J.G. / Ward, T.R.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_database_status.pdb_format_compatible / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_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_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 3.0May 24, 2023Group: Derived calculations / Non-polymer description / Category: chem_comp / struct_conn
Item: _chem_comp.formula / _struct_conn.pdbx_leaving_atom_flag
Revision 4.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 4.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)30,3238
Polymers29,2651
Non-polymers1,0587
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint10 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.172, 73.959, 74.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29265.066 Da / Num. of mol.: 1 / Mutation: N67G, E69R, I91C
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, cyanamide hydratase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VKZ / 4-[2-(4-azanyl-9-chloranyl-2',3',4',5',6'-pentamethyl-7-oxidanylidene-spiro[1$l^{4},8-diaza-9$l^{8}-iridabicyclo[4.3.0]nona-1,3,5-triene-9,1'-1$l^{8}-iridapentacyclo[2.2.0.0^{1,3}.0^{1,5}.0^{2,6}]hexane]-8-yl)ethyl]benzenesulfonamide


Mass: 682.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30ClIrN4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8.0, 0.2 M lithium chloride, 20% w/v polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.769→42.17 Å / Num. obs: 23598 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.988 / Rmerge(I) obs: 0.411 / Net I/σ(I): 6.7
Reflection shellResolution: 1.769→1.8 Å / Redundancy: 12.6 % / Rmerge(I) obs: 2.206 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1304 / CC1/2: 0.48 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QFU

6qfu


Resolution: 1.769→37.508 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.15 / SU B: 3.515 / SU ML: 0.105 / Average fsc free: 0.8978 / Average fsc work: 0.9172 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2233 1158 4.918 %
Rwork0.1781 22386 -
all0.18 --
obs-23544 99.936 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.383 Å20 Å2-0 Å2
2--0.244 Å20 Å2
3---0.139 Å2
Refinement stepCycle: LAST / Resolution: 1.769→37.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 57 216 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132169
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171974
X-RAY DIFFRACTIONr_angle_refined_deg2.9891.7952969
X-RAY DIFFRACTIONr_angle_other_deg1.3081.5884575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6935259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13923.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8815349
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg40.754151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.184158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022426
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02478
X-RAY DIFFRACTIONr_nbd_refined0.1890.2410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21845
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21018
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2963
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2164
X-RAY DIFFRACTIONr_metal_ion_refined0.10.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.211
X-RAY DIFFRACTIONr_nbd_other0.1960.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2390.215
X-RAY DIFFRACTIONr_mcbond_it1.0241.3681033
X-RAY DIFFRACTIONr_mcbond_other1.0231.3681032
X-RAY DIFFRACTIONr_mcangle_it1.6422.0481293
X-RAY DIFFRACTIONr_mcangle_other1.6412.0481294
X-RAY DIFFRACTIONr_scbond_it1.7871.5951136
X-RAY DIFFRACTIONr_scbond_other1.7861.5961137
X-RAY DIFFRACTIONr_scangle_it2.8962.2911656
X-RAY DIFFRACTIONr_scangle_other2.8952.2921657
X-RAY DIFFRACTIONr_lrange_it4.15616.482462
X-RAY DIFFRACTIONr_lrange_other4.05916.1822421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.769-1.8150.313900.2651612X-RAY DIFFRACTION99.5322
1.815-1.8650.31760.2481571X-RAY DIFFRACTION100
1.865-1.9190.34800.2781572X-RAY DIFFRACTION100
1.919-1.9780.231770.2311478X-RAY DIFFRACTION100
1.978-2.0430.213820.1961453X-RAY DIFFRACTION100
2.043-2.1140.198570.1811442X-RAY DIFFRACTION100
2.114-2.1940.259780.1851355X-RAY DIFFRACTION100
2.194-2.2840.339890.2281273X-RAY DIFFRACTION100
2.284-2.3850.242590.1711287X-RAY DIFFRACTION100
2.385-2.5010.207530.1751224X-RAY DIFFRACTION100
2.501-2.6370.242710.1541155X-RAY DIFFRACTION100
2.637-2.7960.257480.1591095X-RAY DIFFRACTION100
2.796-2.9890.196470.161038X-RAY DIFFRACTION100
2.989-3.2280.207380.159978X-RAY DIFFRACTION99.9017
3.228-3.5360.159620.144883X-RAY DIFFRACTION100
3.536-3.9520.172410.138812X-RAY DIFFRACTION100
3.952-4.5610.162300.13734X-RAY DIFFRACTION100
4.561-5.5810.18320.151625X-RAY DIFFRACTION100
5.581-7.8710.238280.17498X-RAY DIFFRACTION100
7.871-37.5080.134200.16301X-RAY DIFFRACTION99.6894

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