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- PDB-5e2n: Crystal structure of human carbonic anhydrase isozyme XIII with 3... -

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Basic information

Entry
Database: PDB / ID: 5e2n
TitleCrystal structure of human carbonic anhydrase isozyme XIII with 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
ComponentsCarbonic anhydrase 13
KeywordsLYASE / 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
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Chem-V14 / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsManakova, E. / Smirnov, A. / Grazulis, S.
CitationJournal: ChemMedChem / Year: 2017
Title: Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases.
Authors: Zubriene, A. / Smirnov, A. / Dudutiene, V. / Timm, D.D. / Matuliene, J. / Michailoviene, V. / Zaksauskas, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 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

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Assembly

Deposited unit
A: Carbonic anhydrase 13
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,97915
Polymers59,2272
Non-polymers1,75313
Water8,701483
1
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4788
Polymers29,6131
Non-polymers8647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5027
Polymers29,6131
Non-polymers8886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.087, 57.597, 159.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29613.318 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase XIII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N1Q1, carbonic anhydrase

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Non-polymers , 6 types, 496 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Fragment: 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Fragment: CITRATE ANION / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-V14 / 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 444.489 Da / Num. of mol.: 2 / Fragment: DI(HYDROXYETHYL)ETHER / Source method: obtained synthetically / Formula: C16H23F3N2O5S2
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Fragment: ZN / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.15 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystallization buffer: 0.1M sodium citrate (pH 5.5), 0.1M sodium acetate (pH 4.5) and 26% PEG4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.53→57.597 Å / Num. obs: 78022 / % possible obs: 98.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 19.548 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Rsym value: 0.05 / Net I/av σ(I): 6.85 / Net I/σ(I): 18.8 / Num. measured all: 506810
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.53-1.615.20.3580.2912.754154104130.150.360.29114.591.4
1.61-1.716.90.2580.2193.574017107660.10.260.2197.299.9
1.71-1.836.60.1670.145.466927101440.060.170.1410.299.9
1.83-1.986.80.1070.098.16455394810.040.110.0915.199.9
1.98-2.166.80.0790.06610.45917687490.030.080.06620.599.9
2.16-2.426.60.0630.05312.15262379590.020.060.05325.3100
2.42-2.796.80.0550.046134766970230.020.050.04629.8100
2.79-3.426.70.0490.04113.43992360020.020.050.04135.3100
3.42-4.846.50.0470.0413.43068847370.020.050.0439.3100
4.84-57.66.20.0490.04111.71708027480.020.050.04137.9100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.006data extraction
REFMAC5.6.0117refinement
XDSdata reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QSJ

4qsj


Resolution: 1.53→54.18 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.866 / SU R Cruickshank DPI: 0.086 / SU Rfree: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 7856 10.1 %RANDOM
Rwork0.176 70076 --
obs0.18 77932 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.93 Å2 / Biso mean: 22.272 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.53→54.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 106 483 4697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.024446
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9656073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40324.271199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43615693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7551519
X-RAY DIFFRACTIONr_chiral_restr0.1690.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213454
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 430 -
Rwork0.262 4329 -
all-4759 -
obs--82.62 %

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