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- PDB-6r6y: Crystal structure of human carbonic anhydrase isozyme XII with 4-... -

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Basic information

Entry
Database: PDB / ID: 6r6y
TitleCrystal structure of human carbonic anhydrase isozyme XII with 4-chloro-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / 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-EA3 / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
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
DepositionMar 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_contact_author ...database_2 / pdbx_contact_author / pdbx_database_proc / 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
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)122,15522
Polymers119,6694
Non-polymers2,48618
Water20,7171150
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,14012
Polymers59,8352
Non-polymers1,30510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,01610
Polymers59,8352
Non-polymers1,1818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.335, 74.192, 91.634
Angle α, β, γ (deg.)90.000, 108.650, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimers:

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 29917.318 Da / Num. of mol.: 4 / Fragment: human carbonic anhydrase XII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O43570, carbonic anhydrase

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Non-polymers , 5 types, 1168 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Fragment: 4-chloro-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-EA3 / 4-chloranyl-2-cyclohexylsulfanyl-~{N}-(2-hydroxyethyl)-5-sulfamoyl-benzamide


Mass: 392.921 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21ClN2O4S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: Crystallization buffer: 0.1M ammonium citrate (pH 7.2), 0.2 M ammonium sulfate and 26% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97552 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97552 Å / Relative weight: 1
ReflectionResolution: 1.38→74.192 Å / Num. all: 198797 / Num. obs: 198797 / % possible obs: 98.8 % / Redundancy: 6.9 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Rsym value: 0.049 / Net I/av σ(I): 7.25 / Net I/σ(I): 18.1 / Num. measured all: 1363773
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.38-1.456.70.3432.1290010.1560.4060.34398.8
1.45-1.546.80.2243.1273460.1020.2660.22498.8
1.54-1.656.80.1494.8257440.0690.1790.14998.7
1.65-1.786.80.17.1238820.0460.1210.198.7
1.78-1.956.80.06710219580.0310.0820.06798.1
1.95-2.1870.0512.6200210.0230.0610.0599
2.18-2.5270.04314177270.020.0530.04399.4
2.52-3.0970.03814.7150650.0180.0460.03899.4
3.09-4.3670.03315.3116240.0150.0390.03399
4.36-74.1926.80.03211.664290.0150.0390.03298.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JD0

1jd0


Resolution: 1.38→73.28 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU R Cruickshank DPI: 0.0618 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.063
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 19765 9.9 %RANDOM
Rwork0.1616 ---
obs0.1641 198753 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 64.89 Å2 / Biso mean: 17.0663 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.16 Å2
2---0.06 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.38→73.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 140 1150 9680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0129027
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.65212317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07951090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4823.504488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.525151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0931536
X-RAY DIFFRACTIONr_chiral_restr0.1190.21112
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027186
X-RAY DIFFRACTIONr_mcbond_it1.5561.3684300
X-RAY DIFFRACTIONr_mcangle_it2.2982.0485410
X-RAY DIFFRACTIONr_scbond_it2.8581.6554727
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 1481 -
Rwork0.194 13214 -
all-14695 -
obs--98.7 %

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