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Basic information

Entry
Database: PDB / ID: 5flo
TitleNative state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination
ComponentsCARBONIC ANHYDRASE 2
KeywordsLYASE / 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 / 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 / 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 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-J4K / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
DepositionOct 28, 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_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_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_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)29,5653
Polymers29,2891
Non-polymers2762
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.753, 41.493, 71.660
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CARBONIC ANHYDRASE 2 / / CARBONATE DEHYDRATASE II / CARBONIC ANHYDRASE C / CAC / CARBONIC ANHYDRASE II / CA-II / HUMAN ...CARBONATE DEHYDRATASE II / CARBONIC ANHYDRASE C / CAC / CARBONIC ANHYDRASE II / CA-II / HUMAN CARBONIC ANHYDRASE 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-J4K / 5-[(4-chloranylphenoxy)methyl]-1H-1,2,3,4-tetrazole


Mass: 210.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7ClN4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 42.1 % / 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: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.66→41.5 Å / Num. obs: 28587 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.7 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CQ0
Resolution: 1.66→69.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.036 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SOME EXTRA UNMODELLED DENSITY SEEN
RfactorNum. reflection% reflectionSelection details
Rfree0.21513 1393 4.9 %RANDOM
Rwork0.15831 ---
obs0.16101 27163 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2---0.1 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.66→69.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 15 240 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192237
X-RAY DIFFRACTIONr_bond_other_d0.0070.022069
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9523049
X-RAY DIFFRACTIONr_angle_other_deg1.0734806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0045280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61625.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.512157
X-RAY DIFFRACTIONr_chiral_restr0.1170.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212612
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02522
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_it2.1261.6531087
X-RAY DIFFRACTIONr_mcbond_other2.1271.651086
X-RAY DIFFRACTIONr_mcangle_it3.0332.7791375
X-RAY DIFFRACTIONr_mcangle_other3.0322.7831376
X-RAY DIFFRACTIONr_scbond_it3.0061.9991150
X-RAY DIFFRACTIONr_scbond_other3.00321148
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.333.1841674
X-RAY DIFFRACTIONr_long_range_B_refined5.2369.80210135
X-RAY DIFFRACTIONr_long_range_B_other5.2369.80310136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.663→1.707 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 106 -
Rwork0.213 1875 -
obs--94.33 %

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