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- PDB-6qn0: Three dimensional structure of human carbonic anhydrase XII in co... -

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Basic information

Entry
Database: PDB / ID: 6qn0
TitleThree dimensional structure of human carbonic anhydrase XII in complex with benzenesulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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-J8Q / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsDvinskis, E. / Leitans, J. / Tars, K.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Paketuryte, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Manakova, E. / Grazulis, S. / Tars, K. / Matulis, D.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 6, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.3Oct 13, 2021Group: Data collection / Category: pdbx_database_proc
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,39812
Polymers119,4294
Non-polymers1,9708
Water13,079726
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6996
Polymers59,7142
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-2 kcal/mol
Surface area21620 Å2
MethodPISA
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6996
Polymers59,7142
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-2 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.760, 74.760, 76.230
Angle α, β, γ (deg.)90.02, 74.32, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Carbonic anhydrase 12 / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 29857.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Production host: Escherichia coli (E. coli) / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-J8Q / ~{N}-butyl-4-chloranyl-2-(2-phenylethylsulfanyl)-5-sulfamoyl-benzamide


Mass: 426.981 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23ClN2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.6, 31% PEG 4000, PROTEIN CONC. 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.89→74.76 Å / Num. obs: 64810 / % possible obs: 83.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 21.92 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 4.6
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2 / Num. unique obs: 9457 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JD0

1jd0


Resolution: 1.89→74.76 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.799 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22458 3232 5 %RANDOM
Rwork0.16476 ---
obs0.16778 61577 83.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.18 Å20.64 Å2
2--1.82 Å20.3 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.89→74.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 0 112 726 9176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138702
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177501
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.65911847
X-RAY DIFFRACTIONr_angle_other_deg1.3791.58217519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97551030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61123.562466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.485151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6561532
X-RAY DIFFRACTIONr_chiral_restr0.0770.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029735
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021821
X-RAY DIFFRACTIONr_mcbond_it1.8272.2354150
X-RAY DIFFRACTIONr_mcbond_other1.8262.2354149
X-RAY DIFFRACTIONr_mcangle_it2.6943.3445167
X-RAY DIFFRACTIONr_mcangle_other2.6943.3445168
X-RAY DIFFRACTIONr_scbond_it2.4892.5124552
X-RAY DIFFRACTIONr_scbond_other2.4892.5134553
X-RAY DIFFRACTIONr_scangle_other3.8773.6586680
X-RAY DIFFRACTIONr_long_range_B_refined5.27426.7359829
X-RAY DIFFRACTIONr_long_range_B_other5.21726.4849705
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 192 -
Rwork0.269 4337 -
obs--78.29 %

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