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- PDB-4knm: Crystal structure of human carbonic anhydrase isozyme XIII with 2... -

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Basic information

Entry
Database: PDB / ID: 4knm
TitleCrystal structure of human carbonic anhydrase isozyme XIII with 2-Chloro-4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide
ComponentsCarbonic anhydrase 13
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / 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
Chem-E1E / TRIETHYLENE GLYCOL / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII
Authors: Capkauskaite, E. / Zubriene, A. / Smirnov, A. / Torresan, J. / Kisonaite, M. / Kazokaite, J. / Gylyte, J. / Michailoviene, V. / Jogaite, V. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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_ref_seq_dif.details / _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 13
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2517
Polymers59,2272
Non-polymers1,0255
Water6,089338
1
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2014
Polymers29,6131
Non-polymers5873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0513
Polymers29,6131
Non-polymers4372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.591, 58.165, 71.075
Angle α, β, γ (deg.)90.000, 92.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 13 / Carbonate dehydratase XIII / Carbonic anhydrase XIII / CA-XIII


Mass: 29613.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N1Q1, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E1E / 2-chloro-4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide


Mass: 371.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14ClN3O3S2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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 Å3/Da / Density % sol: 39.4 % / Mosaicity: 0.6 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium citrate (pH 5.5), 0.1M sodium acetate (pH 4.5), 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 2, 2011
RadiationMonochromator: VARIMAX-HF MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20.542 Å / Num. obs: 37114 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 25.023 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-240.6220.4671.32146653740.30.620.4672.999
2-2.124.10.4030.3022.12073350720.190.40.3024.899.6
2.12-2.274.20.2960.2272.82002048020.140.30.2277.299.8
2.27-2.454.30.2130.1643.91916744870.10.210.16410.6100
2.45-2.694.40.1520.1175.41786441060.070.150.11714.8100
2.69-34.40.110.0847.61644637620.050.110.08420100
3-3.474.40.0780.06110.51447133040.040.080.06128.3100
3.47-4.254.40.0630.04912.61238728150.030.060.04938100
4.25-6.014.40.0570.04513.5956721840.030.060.04541.3100
6.01-20.543.90.0850.0624.9467912080.050.090.06239.697.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
DNAdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NNO

2nno


Resolution: 1.9→20.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.851 / SU R Cruickshank DPI: 0.194 / SU Rfree: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3653 9.8 %RANDOM
Rwork0.178 ---
all0.184 37099 --
obs0.184 37099 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.85 Å2 / Biso mean: 21.671 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.8 Å2
2---0.36 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 58 338 4512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0214380
X-RAY DIFFRACTIONr_angle_refined_deg1.9881.9585978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3185533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9324.121199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28215700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.41520
X-RAY DIFFRACTIONr_chiral_restr0.1460.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023408
X-RAY DIFFRACTIONr_nbd_refined0.210.22118
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2343
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.233
X-RAY DIFFRACTIONr_mcbond_it1.1921.52641
X-RAY DIFFRACTIONr_mcangle_it1.91224295
X-RAY DIFFRACTIONr_scbond_it2.92731739
X-RAY DIFFRACTIONr_scangle_it4.2514.51683
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 261 -
Rwork0.288 2441 -
all-2702 -
obs--98.87 %

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