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- PDB-6s9z: Expression tag modified N-terminus of human Carbonic Anhydrase II... -

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Basic information

Entry
Database: PDB / ID: 6s9z
TitleExpression tag modified N-terminus of human Carbonic Anhydrase II covalently linked to fragment
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 conversion
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
(4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Chem-VKL / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.
Authors: Glockner, S. / Heine, A. / Klebe, G.
History
DepositionJul 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 2.0May 24, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _pdbx_entry_details.has_protein_modification

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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)30,9989
Polymers29,8071
Non-polymers1,1928
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-78 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.354, 41.280, 72.421
Angle α, β, γ (deg.)90.000, 104.651, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 8 types, 246 molecules

#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID;(4-carboxyphenyl)-chloranyl-mercury


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2 / Comment: protease inhibitor*YM
#7: Chemical ChemComp-VKL / 3-[3,4-bis(fluoranyl)phenyl]-5-methyl-1$l^{4},4,5$l^{4},7-tetrazabicyclo[4.3.0]nona-1(6),2,4-triene


Mass: 250.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12F2N4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: Ammonium sulfate 2.7 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 0.95→41.28 Å / Num. obs: 141261 / % possible obs: 92.7 % / Redundancy: 3.83 % / Biso Wilson estimate: 6.95 Å2 / CC1/2: 0.998 / Rsym value: 0.063 / Net I/σ(I): 10.69
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 3.75 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 19435 / CC1/2: 0.798 / Rsym value: 0.432 / % possible all: 79

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 0.95→35.03 Å / SU ML: 0.063 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.0719
RfactorNum. reflection% reflection
Rfree0.1365 7061 5 %
Rwork0.1192 --
obs0.1201 141257 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 9.35 Å2
Refinement stepCycle: LAST / Resolution: 0.95→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 49 238 2370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062777
X-RAY DIFFRACTIONf_angle_d0.97393847
X-RAY DIFFRACTIONf_chiral_restr0.0883386
X-RAY DIFFRACTIONf_plane_restr0.0074550
X-RAY DIFFRACTIONf_dihedral_angle_d14.85271058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.960.21161530.20732915X-RAY DIFFRACTION60.73
0.96-0.970.22761790.18753398X-RAY DIFFRACTION70.87
0.97-0.980.19262080.17873964X-RAY DIFFRACTION81.64
0.98-10.17112290.16474339X-RAY DIFFRACTION91.67
1-1.010.17462360.15654480X-RAY DIFFRACTION92.13
1.01-1.020.16772330.14724436X-RAY DIFFRACTION93.32
1.02-1.040.16332370.14794506X-RAY DIFFRACTION93.05
1.04-1.050.15612350.13354461X-RAY DIFFRACTION93.19
1.05-1.070.1362350.1244468X-RAY DIFFRACTION93.5
1.07-1.090.14922390.11724537X-RAY DIFFRACTION93.32
1.09-1.110.12512340.11094441X-RAY DIFFRACTION93.69
1.11-1.130.12522360.09724493X-RAY DIFFRACTION94.11
1.13-1.150.11642420.09614601X-RAY DIFFRACTION94.3
1.15-1.170.10842380.0974515X-RAY DIFFRACTION94.72
1.17-1.20.11192380.09634533X-RAY DIFFRACTION94.72
1.2-1.220.11152420.10134582X-RAY DIFFRACTION94.87
1.22-1.260.11842420.10124612X-RAY DIFFRACTION95.1
1.26-1.290.1152420.09994590X-RAY DIFFRACTION95.14
1.29-1.330.12042420.09744595X-RAY DIFFRACTION95.5
1.33-1.370.10932430.14618X-RAY DIFFRACTION95.82
1.37-1.420.12552420.10184604X-RAY DIFFRACTION95.71
1.42-1.480.10752450.10064660X-RAY DIFFRACTION96.5
1.48-1.540.12862450.10344650X-RAY DIFFRACTION96.43
1.54-1.620.11072440.10484624X-RAY DIFFRACTION96.36
1.62-1.730.11432490.10534739X-RAY DIFFRACTION97.4
1.73-1.860.11912480.11164703X-RAY DIFFRACTION97.15
1.86-2.050.12232480.11294715X-RAY DIFFRACTION97.26
2.05-2.340.12242480.1164727X-RAY DIFFRACTION97.07
2.34-2.950.16712530.13184804X-RAY DIFFRACTION98.14
2.95-35.030.17012560.14324886X-RAY DIFFRACTION97.89

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