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- PDB-5lla: Crystal structure of human carbonic anhydrase isozyme XIII with 4... -

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Basic information

Entry
Database: PDB / ID: 5lla
TitleCrystal structure of human carbonic anhydrase isozyme XIII with 4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide
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-6YQ / CITRIC ACID / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Chemistryselect / Year: 2017
Title: Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases
Authors: Capkauskaite, E. / Linkuviene, V. / Smirnov, A. / Milinaviciute, G. / Timm, D. / Kasiliauskaite, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Jan 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.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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,56510
Polymers59,2272
Non-polymers1,3398
Water9,908550
1
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2835
Polymers29,6131
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2835
Polymers29,6131
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.023, 57.276, 159.284
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 BA

#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

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Non-polymers , 5 types, 558 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6YQ / 4-[2-(benzimidazol-1-yl)ethanoyl]-2-chloranyl-benzenesulfonamide


Mass: 349.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClN3O3S
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.16 Å3/Da / Density % sol: 42.99 % / Mosaicity: 0.17 °
Crystal growTemperature: 291 K / Method: evaporation
Details: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.1M sodium acetate (pH 4.5) and 26% PEG3350

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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: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.5→159.284 Å / Num. all: 82297 / Num. obs: 82297 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Rsym value: 0.033 / Net I/av σ(I): 15.123 / Net I/σ(I): 26.8 / Num. measured all: 524723
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.586.60.3582.2199.2
1.58-1.686.40.2493199.4
1.68-1.796.40.1514.9199.3
1.79-1.946.60.0848.9199.8
1.94-2.126.20.05114.5199.2
2.12-2.376.60.03719.6199.7
2.37-2.746.10.02923.8199.4
2.74-3.356.40.02327.2199.1
3.35-4.745.90.01931.5198.5
4.74-159.2845.80.01732.7198.2

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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: 4KNN

4knn


Resolution: 1.5→79.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 8196 10 %RANDOM
Rwork0.1787 ---
obs0.1821 74022 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 82.81 Å2 / Biso mean: 20.079 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 1.5→79.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 82 550 4740
Biso mean--41.03 28.89 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.024440
X-RAY DIFFRACTIONr_angle_refined_deg2.4521.9626067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5995542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96724.039203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70615705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3431522
X-RAY DIFFRACTIONr_chiral_restr0.2330.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213490
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 591 -
Rwork0.352 5398 -
all-5989 -
obs--98.99 %

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