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- PDB-6g5u: Crystal structure of human carbonic anhydrase isozyme XIII with N... -

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Basic information

Entry
Database: PDB / ID: 6g5u
TitleCrystal structure of human carbonic anhydrase isozyme XIII with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide
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
CITRIC ACID / Chem-ENN / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Kisonaite, M. / Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionMar 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,38610
Polymers59,2272
Non-polymers1,1608
Water10,935607
1
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1285
Polymers29,6131
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2585
Polymers29,6131
Non-polymers6454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.790, 58.305, 160.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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 BL21(DE3) (bacteria) / References: UniProt: Q8N1Q1, carbonic anhydrase

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Non-polymers , 5 types, 615 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Fragment: N-butyl-2,4-dichloro-5-sulfamoyl-benzamide / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ENN / ~{N}-butyl-2,4-bis(chloranyl)-5-sulfamoyl-benzamide


Mass: 325.211 Da / Num. of mol.: 2 / Fragment: ZN / Source method: obtained synthetically / Formula: C11H14Cl2N2O3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.22 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Crystallization buffer: 0.1M ammonium citrate (pH 5.0) and 18% PEG 4000

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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: Feb 19, 2014
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: 1.7→40.309 Å / Num. all: 57444 / Num. obs: 57444 / % possible obs: 98.2 % / Redundancy: 4.6 % / Rpim(I) all: 0.066 / Rrim(I) all: 0.145 / Rsym value: 0.121 / Net I/av σ(I): 3.957 / Net I/σ(I): 6.6 / Num. measured all: 265748
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.7-1.795.10.4441.40.230.5390.444100
1.79-1.95.10.3551.70.1880.4390.355100
1.9-2.0350.2612.20.1450.3310.261100
2.03-2.195.10.11160.060.1380.111100
2.19-2.44.70.15730.0910.20.15798.8
2.4-2.694.50.0817.30.0450.0980.08199.7
2.69-3.14.10.0717.80.0390.0840.07197.1
3.1-3.83.70.0766.90.0450.0910.07693.4
3.8-5.3830.059.70.0310.060.0589
5.38-40.3093.30.058.70.0310.0620.0592

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.1data extraction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLA

5lla


Resolution: 1.7→40.19 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.1335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5727 10.1 %RANDOM
Rwork0.1924 ---
obs0.1961 56867 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 78.83 Å2 / Biso mean: 16.5456 Å2 / Biso min: 3.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.39 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 65 607 4780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194355
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9595935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18624.171199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29915698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0631520
X-RAY DIFFRACTIONr_chiral_restr0.1510.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213388
X-RAY DIFFRACTIONr_mcbond_it1.4041.3662097
X-RAY DIFFRACTIONr_mcangle_it2.1292.0432630
X-RAY DIFFRACTIONr_scbond_it2.5391.6212258
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 428 -
Rwork0.28 3847 -
all-4275 -
obs--99.93 %

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