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- PDB-7puv: Crystal structure of carbonic anhydrase XII with methyl 2-(benzen... -

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Basic information

Entry
Database: PDB / ID: 7puv
TitleCrystal structure of carbonic anhydrase XII with methyl 2-(benzenesulfonyl)-4-chloro-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 / one-carbon metabolic process / 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-84Z / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.3Oct 23, 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)122,03120
Polymers119,6694
Non-polymers2,36216
Water20,5911143
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,03710
Polymers59,8352
Non-polymers1,2038
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)60,99310
Polymers59,8352
Non-polymers1,1598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.434, 74.460, 91.913
Angle α, β, γ (deg.)90.000, 108.950, 90.000
Int Tables number4
Space group name H-MP1211

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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 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

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Non-polymers , 5 types, 1159 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-84Z / methyl 4-chloranyl-2-(phenylsulfonyl)-5-sulfamoyl-benzoate


Mass: 389.831 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12ClNO6S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1143 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.27 %
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: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.399→86.933 Å / Num. all: 189636 / Num. obs: 189636 / % possible obs: 97.6 % / Redundancy: 4.2 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.112 / Rsym value: 0.08 / Net I/av σ(I): 2.3 / Net I/σ(I): 11.4 / Num. measured all: 801850
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
1.4-1.483.50.158484178240430.1070.2140.1585.585.2
1.48-1.564.30.1314.5115244266390.0830.1770.1317.599.7
1.56-1.674.10.1075.3104085250980.070.1460.1078.799.7
1.67-1.814.40.095.8103208233850.0580.1240.0910.799.8
1.81-1.984.20.0776.189958214960.0510.1070.07712.399.7
1.98-2.214.50.0726.187645195180.0460.10.07214.699.9
2.21-2.554.30.075.773924172340.0470.0990.0715.199.8
2.55-3.134.60.0715.266710145660.0460.10.07116.799.9
3.13-4.434.40.0774.549387113370.0510.1080.07717.699.8
4.43-86.9334.40.093.42751163200.0580.1250.0916.999.9

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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: 1.4→73.24 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.217 18914 10 %RANDOM
Rwork0.1592 ---
obs0.1649 170686 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.02 Å2 / Biso mean: 18.536 Å2 / Biso min: 5.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0.07 Å2
2--2.17 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.4→73.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 135 1143 9614
Biso mean--17.7 28.65 -
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0128941
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.65112213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45151085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70423.708472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.621151377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6181531
X-RAY DIFFRACTIONr_chiral_restr0.2210.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.027111
X-RAY DIFFRACTIONr_rigid_bond_restr7.39638941
X-RAY DIFFRACTIONr_sphericity_free26.5125708
X-RAY DIFFRACTIONr_sphericity_bonded17.81159109
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.254 1016 -
Rwork0.166 9197 -
obs--71.24 %

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