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- PDB-6sac: N-terminal expression tag remainder of human Carbonic Anhydrase I... -

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Basic information

Entry
Database: PDB / ID: 6sac
TitleN-terminal expression tag remainder of human Carbonic Anhydrase II covalently modified by fragment
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 conversion / fragment
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 / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / 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
1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine / (4-CARBOXYPHENYL)(CHLORO)MERCURY / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 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 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_symmetry
Revision 1.2Nov 6, 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)31,06710
Polymers29,8071
Non-polymers1,2619
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-75 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.374, 41.286, 72.281
Angle α, β, γ (deg.)90.000, 104.823, 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, 207 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-47J / 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine


Mass: 125.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 40.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 Mte, Tris 0.1 M, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.02→40.964 Å / Num. obs: 121056 / % possible obs: 98.3 % / Redundancy: 2.72 % / Biso Wilson estimate: 8.47 Å2 / CC1/2: 0.998 / Rsym value: 0.053 / Net I/σ(I): 9.99
Reflection shellResolution: 1.02→1.08 Å / Redundancy: 2.53 % / Mean I/σ(I) obs: 2.15 / Num. unique obs: 19033 / CC1/2: 0.78 / Rsym value: 0.391 / % possible all: 96

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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: 1.02→31.95 Å / SU ML: 0.0715 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.45
RfactorNum. reflection% reflectionSelection details
Rfree0.1418 6049 5 %Random selection of 5 %
Rwork0.126 ---
obs0.1268 121032 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.76 Å2
Refinement stepCycle: LAST / Resolution: 1.02→31.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 47 198 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782627
X-RAY DIFFRACTIONf_angle_d1.06643628
X-RAY DIFFRACTIONf_chiral_restr0.0889368
X-RAY DIFFRACTIONf_plane_restr0.0083507
X-RAY DIFFRACTIONf_dihedral_angle_d13.2624973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.02-1.030.22861890.22453596X-RAY DIFFRACTION92.36
1.03-1.040.22121930.2173673X-RAY DIFFRACTION95.13
1.04-1.060.20621990.19453766X-RAY DIFFRACTION96.21
1.06-1.070.19271980.17663760X-RAY DIFFRACTION97.97
1.07-1.080.17722000.15283818X-RAY DIFFRACTION98.55
1.08-1.10.15232010.14253816X-RAY DIFFRACTION98.53
1.1-1.110.14792040.14023872X-RAY DIFFRACTION98.84
1.11-1.130.14461990.12913787X-RAY DIFFRACTION99.03
1.13-1.150.14332040.12413862X-RAY DIFFRACTION99
1.15-1.170.14921990.11853789X-RAY DIFFRACTION98.57
1.17-1.190.13252030.11623849X-RAY DIFFRACTION98.59
1.19-1.210.1332030.11373870X-RAY DIFFRACTION99.2
1.21-1.230.12812020.10833833X-RAY DIFFRACTION99.24
1.23-1.260.12122030.10553854X-RAY DIFFRACTION99.05
1.26-1.280.13492030.10723865X-RAY DIFFRACTION99.22
1.28-1.310.13892020.10593820X-RAY DIFFRACTION99.28
1.31-1.350.12662040.10543875X-RAY DIFFRACTION99.22
1.35-1.380.13412020.1053853X-RAY DIFFRACTION99.24
1.38-1.420.14252040.10723860X-RAY DIFFRACTION99.12
1.42-1.470.12782040.10113884X-RAY DIFFRACTION99.25
1.47-1.520.11842030.10373856X-RAY DIFFRACTION99.46
1.52-1.580.11652030.10183873X-RAY DIFFRACTION99.27
1.58-1.660.12662030.10343859X-RAY DIFFRACTION99.15
1.66-1.740.12142030.1093859X-RAY DIFFRACTION98.83
1.74-1.850.13012030.11243862X-RAY DIFFRACTION98.4
1.85-20.12722030.11583843X-RAY DIFFRACTION98.49
2-2.20.13522030.11763867X-RAY DIFFRACTION98.67
2.2-2.510.13752040.12613867X-RAY DIFFRACTION98.48
2.51-3.170.1492040.1413888X-RAY DIFFRACTION98.01
3.17-31.950.15872040.14833907X-RAY DIFFRACTION96.64

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