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- PDB-5ekj: Human Carbonic Anhydrase II complexed with a two-faced guest -

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Basic information

Entry
Database: PDB / ID: 5ekj
TitleHuman Carbonic Anhydrase II complexed with a two-faced guest
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / LYASE-LYASE INHIBITOR complex
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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-TG4 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.129 Å
AuthorsRoose, B.W. / Dmochowski, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097478 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Programming A Molecular Relay for Ultrasensitive Biodetection through (129) Xe NMR.
Authors: Wang, Y. / Roose, B.W. / Philbin, J.P. / Doman, J.L. / Dmochowski, I.J.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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)29,7675
Polymers29,2731
Non-polymers4944
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-12 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 41.350, 72.130
Angle α, β, γ (deg.)90.000, 104.150, 90.000
Int Tables number4
Space group name H-MP1211

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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: 29273.062 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pCAM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 276 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TG4 / 2-(butylamino)-~{N}-[2-(4-sulfamoylphenyl)ethyl]ethanamide


Mass: 313.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N3O3S
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 50 mM Tris, pH 7.0, 1.3 M sodium citrate / PH range: 7.0-8.0 / Temp details: Transferred to 294K after 3 weeks at 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.129→41.35 Å / Num. all: 90974 / Num. obs: 87598 / % possible obs: 96.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 6.49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Net I/σ(I): 17.4 / Num. measured all: 631318 / Scaling rejects: 521
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.129-1.156.10.3997.42556941930.9220.17692.8
6.18-41.355.80.05228.732775670.9930.02694.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.14data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.129→39.93 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 11.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1505 4444 5.08 %Random selection
Rwork0.1344 83145 --
obs0.1352 87589 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.34 Å2 / Biso mean: 10.7384 Å2 / Biso min: 3.23 Å2
Refinement stepCycle: final / Resolution: 1.129→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 29 272 2324
Biso mean--12.52 21.75 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052136
X-RAY DIFFRACTIONf_angle_d1.192911
X-RAY DIFFRACTIONf_chiral_restr0.05303
X-RAY DIFFRACTIONf_plane_restr0.006381
X-RAY DIFFRACTIONf_dihedral_angle_d12.67770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.129-1.14180.17622920.13365221551392
1.1418-1.15530.14753160.12845289560595
1.1553-1.16940.11832580.12285342560094
1.1694-1.18420.12813320.11355271560394
1.1842-1.19980.12713040.11465238554295
1.1998-1.21620.1242930.11115372566594
1.2162-1.23360.14783030.11065298560195
1.2336-1.2520.11712830.11155384566795
1.252-1.27150.15162730.1165370564395
1.2715-1.29240.13812800.11215429570995
1.2924-1.31470.11982640.10835408567296
1.3147-1.33860.12352990.11345398569796
1.3386-1.36430.13823110.11255385569695
1.3643-1.39220.13452550.11665466572197
1.3922-1.42250.14033090.11815447575696
1.4225-1.45550.15182750.11715396567196
1.4555-1.49190.13452810.11795486576798
1.4919-1.53230.14172990.1185512581197
1.5323-1.57740.13952950.11885475577097
1.5774-1.62830.15122730.12555543581697
1.6283-1.68650.13923000.12495507580798
1.6865-1.7540.14682540.1335542579698
1.754-1.83380.17012620.13755582584498
1.8338-1.93050.14963100.14055596590699
1.9305-2.05150.15182950.13615553584899
2.0515-2.20990.15393450.14675532587799
2.2099-2.43220.17193020.14855616591899
2.4322-2.78410.18252840.165756255909100
2.7841-3.50730.17222850.15556405925100
3.5073-39.95480.14783080.14615496580498

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