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Basic information

Entry
Database: PDB / ID: 5fnk
TitleNative state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / FRAGMENTS / CARBONIC ANHYDRASE / METALLOPROTEIN
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / 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 / cytoplasm / cytosol
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
(~{E})-3-(2,4-dichlorophenyl)prop-2-enoic acid / ACETIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsWoods, L.A. / Dolezal, O. / Ren, B. / Ryan, J.H. / Peat, T.S. / Poulsen, S.A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Native State Mass Spectrometry, Surface Plasmon Resonance and X-Ray Crystallography Correlate Strongly as a Fragment Screening Combination.
Authors: Woods, L. / Dolezal, O. / Ren, B. / Ryan, J.H. / Peat, T.S. / Poulsen, S.
History
DepositionNov 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,7567
Polymers29,2891
Non-polymers4676
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 41.516, 72.157
Angle α, β, γ (deg.)90.00, 104.42, 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: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 6 types, 289 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-5OO / (~{E})-3-(2,4-dichlorophenyl)prop-2-enoic acid


Mass: 217.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6Cl2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.59→41.5 Å / Num. obs: 33070 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.8
Reflection shellResolution: 1.59→1.61 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CQ0

4cq0


Resolution: 1.59→69.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.604 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY DENSITY FOR FRAGMENT IS WEAKER THAN MOST OF THE OTHERS AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY DENSITY FOR FRAGMENT IS WEAKER THAN MOST OF THE OTHERS AND THE COMPOUND IS MODELLED AT 0.8 OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.19522 1647 5 %RANDOM
Rwork0.14675 ---
obs0.14909 31410 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.59→69.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 24 283 2366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192249
X-RAY DIFFRACTIONr_bond_other_d0.0030.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.9543059
X-RAY DIFFRACTIONr_angle_other_deg1.06534916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10924.554101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15415386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.071158
X-RAY DIFFRACTIONr_chiral_restr0.1220.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212590
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02526
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_it1.8311.5031088
X-RAY DIFFRACTIONr_mcbond_other1.8321.4971086
X-RAY DIFFRACTIONr_mcangle_it2.6192.5261375
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9391.8911161
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.586→1.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 119 -
Rwork0.219 2154 -
obs--93.58 %

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