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- PDB-7puw: Crystal structure of carbonic anhydrase XII with methyl 2-chloro-... -

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Basic information

Entry
Database: PDB / ID: 7puw
TitleCrystal structure of carbonic anhydrase XII with methyl 2-chloro-4-[(2-phenylethyl)sulfanyl]-5-sulfamoylbenzoate
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 / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
Chem-84I / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2021
Title: Methyl 2-Halo-4-Substituted-5-Sulfamoyl-Benzoates as High Affinity and Selective Inhibitors of Carbonic Anhydrase IX.
Authors: Zaksauskas, A. / Capkauskaite, E. / Paketuryte-Latve, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Stancaitis, L. / Mickeviciute, A. / Jachno, J. / Jezepcikas, L. / ...Authors: Zaksauskas, A. / Capkauskaite, E. / Paketuryte-Latve, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Stancaitis, L. / Mickeviciute, A. / Jachno, J. / Jezepcikas, L. / Linkuviene, V. / Sakalauskas, A. / Manakova, E. / Grazulis, S. / Matuliene, J. / Tars, K. / Matulis, D.
History
DepositionSep 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)121,72316
Polymers119,6694
Non-polymers2,05312
Water19,2941071
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8618
Polymers59,8352
Non-polymers1,0276
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)60,8618
Polymers59,8352
Non-polymers1,0276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.257, 74.155, 91.655
Angle α, β, γ (deg.)90.000, 108.750, 90.000
Int Tables number4
Space group name H-MP1211

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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: 29917.318 Da / Num. of mol.: 4 / Fragment: Human Carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / 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-84I / methyl 2-chloranyl-4-(2-phenylethylsulfanyl)-5-sulfamoyl-benzoate


Mass: 385.886 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16ClNO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1071 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M ammonium citrate (pH 7.0), 0.2 M ammonium sulfate and 30% 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: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.418→86.789 Å / Num. all: 181236 / Num. obs: 181236 / % possible obs: 97.7 % / Redundancy: 6.6 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Rsym value: 0.058 / Net I/av σ(I): 4.2 / Net I/σ(I): 16.5 / Num. measured all: 1201771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.42-1.495.50.2612.8126370231570.1320.3190.261585.9
1.49-1.586.80.1913.8173850254500.0860.2250.1917.899.7
1.58-1.696.50.135.4156404239790.0610.1560.131099.7
1.69-1.8370.0917.3155083222710.0410.1090.09113.799.8
1.83-26.60.0669135254205630.0310.080.06617.899.7
2-2.2470.05510130544186020.0250.0660.05522.699.9
2.24-2.596.70.05110110314164210.0240.0620.05124.899.7
2.59-3.177.10.059.499670139530.0220.0590.0528.999.9
3.17-4.486.80.0518.773246107980.0220.0590.05132.199.8
4.48-86.7896.80.0536.54103660420.0240.0620.05331.499.8

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT2

4ht2


Resolution: 1.42→86.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 18046 10 %RANDOM
Rwork0.1743 ---
obs0.177 163154 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.58 Å2 / Biso mean: 20.327 Å2 / Biso min: 7.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å20.28 Å2
2---0.19 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.42→86.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8365 0 116 1071 9552
Biso mean--32.66 30.28 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128866
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.6512093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15751068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70923.5480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.916151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5831535
X-RAY DIFFRACTIONr_chiral_restr0.130.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027058
LS refinement shellResolution: 1.42→1.455 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.26 997 -
Rwork0.239 9156 -
obs--74.13 %

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