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- PDB-5lln: Crystal structure of human carbonic anhydrase isozyme XIII with 2... -

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Basic information

Entry
Database: PDB / ID: 5lln
TitleCrystal structure of human carbonic anhydrase isozyme XIII with 2,3,5,6-Tetrafluoro-4-(propylthio)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 / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / 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-3TV / CITRIC ACID / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: To be published
Title: Crystal structure of human carbonic anhydrase isozyme XIII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
Authors: Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,5409
Polymers59,2272
Non-polymers1,3147
Water10,341574
1
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3665
Polymers29,6131
Non-polymers7534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1744
Polymers29,6131
Non-polymers5613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.520, 57.334, 159.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / 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 (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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-3TV / 2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide


Mass: 303.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9F4NO2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Crystallization buffer: 0.1M ammonium citrate (pH 5) and 20% 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-F / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.6→159.708 Å / Num. obs: 69410 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 15.121 Å2 / Rsym value: 0.079 / Net I/av σ(I): 5.718 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.6913.10.2792.7199.9
1.69-1.79130.1953.81100
1.79-1.9112.80.1415.21100
1.91-2.0713.30.1096.41100
2.07-2.2613.50.0917.4199.9
2.26-2.5313.50.0828.11100
2.53-2.9213.20.0748.6199.9
2.92-3.5813.30.0688.8199.9
3.58-5.0612.50.0619.8199.9
5.06-159.70812.40.0539.2199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NNO

2nno


Resolution: 1.6→79.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.0945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 6932 10 %RANDOM
Rwork0.1682 ---
obs0.1719 62389 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 82.59 Å2 / Biso mean: 16.125 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.6→79.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 95 574 4785
Biso mean--31.64 24.81 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.024473
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9636124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44624.078206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2321521
X-RAY DIFFRACTIONr_chiral_restr0.1670.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213521
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 522 -
Rwork0.192 4554 -
all-5076 -
obs--99.84 %

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