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- PDB-5t72: Human carboanhydrase F131C_C206S double mutant in complex with 2 -

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Basic information

Entry
Database: PDB / ID: 5t72
TitleHuman carboanhydrase F131C_C206S double mutant in complex with 2
ComponentsCarbonic anhydrase 2
KeywordsTRANSFERASE / photopharmacology / carbonic anhydrase / photochromic tethered ligand / azobenzene / computational screening
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
4-[(E)-(4-aminophenyl)diazenyl]benzenesulfonamide / 4-(HYDROXYMERCURY)BENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDuBay, K.H. / Iwan, K. / Osorio-Planes, L. / Geissler, P. / Groll, M. / Trauner, D. / Broichhagen, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: A Predictive Approach for the Optical Control of Carbonic Anhydrase II Activity.
Authors: DuBay, K.H. / Iwan, K. / Osorio-Planes, L. / Geissler, P.L. / Groll, M. / Trauner, D. / Broichhagen, J.
History
DepositionSep 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0325
Polymers29,2291
Non-polymers8034
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-2 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 41.190, 72.230
Angle α, β, γ (deg.)90.00, 104.09, 90.00
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: 29228.965 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 375 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6HgO3
#4: Chemical ChemComp-4WA / 4-[(E)-(4-aminophenyl)diazenyl]benzenesulfonamide


Mass: 276.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N4O2S
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3 M (NH4)2SO4, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→15 Å / Num. obs: 50591 / % possible obs: 91.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.7
Reflection shellResolution: 1.3→1.4 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.4 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VVA

2vva


Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.561 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16634 2662 5 %RANDOM
Rwork0.14779 ---
obs0.15062 50591 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.517 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20.09 Å2
2--0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 38 371 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192161
X-RAY DIFFRACTIONr_bond_other_d0.0030.022035
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9752932
X-RAY DIFFRACTIONr_angle_other_deg1.28934708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37524.74297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1615352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.946157
X-RAY DIFFRACTIONr_chiral_restr0.1310.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.1571028
X-RAY DIFFRACTIONr_mcbond_other0.6841.1541026
X-RAY DIFFRACTIONr_mcangle_it0.8781.7361282
X-RAY DIFFRACTIONr_mcangle_other0.8771.7391283
X-RAY DIFFRACTIONr_scbond_it1.0881.3841133
X-RAY DIFFRACTIONr_scbond_other1.0871.3841133
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0711.981651
X-RAY DIFFRACTIONr_long_range_B_refined2.13515.6742506
X-RAY DIFFRACTIONr_long_range_B_other1.79214.6782421
X-RAY DIFFRACTIONr_rigid_bond_restr0.70634196
X-RAY DIFFRACTIONr_sphericity_free16.9715212
X-RAY DIFFRACTIONr_sphericity_bonded5.47754295
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 187 -
Rwork0.217 3553 -
obs--85.68 %

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