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- PDB-7puu: Crystal structure of carbonic anhydrase XII with methyl 4-chloro-... -

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Basic information

Entry
Database: PDB / ID: 7puu
TitleCrystal structure of carbonic anhydrase XII with methyl 4-chloro-2-cyclohexylsulfanyl-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-84O / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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

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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)121,69717
Polymers119,6694
Non-polymers2,02713
Water20,0691114
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94110
Polymers59,8352
Non-polymers1,1078
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)60,7557
Polymers59,8352
Non-polymers9215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.321, 74.127, 91.588
Angle α, β, γ (deg.)90.000, 108.790, 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-84O / methyl 4-chloranyl-2-cyclohexylsulfanyl-5-sulfamoyl-benzoate


Mass: 363.880 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H18ClNO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 1114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 40.76 %
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: 1.506→86.704 Å / Num. all: 145217 / Num. obs: 145217 / % possible obs: 94 % / Redundancy: 6.9 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Rsym value: 0.038 / Net I/av σ(I): 9.2 / Net I/σ(I): 25.2 / Num. measured all: 1005480
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
1.51-1.596.30.1684.5103135164170.0790.2030.1688.273.2
1.59-1.687.20.1275.9146872204970.0560.1510.12711.596.2
1.68-1.86.80.0888.3130787192670.0410.1080.08814.796.5
1.8-1.947.20.06310.9130369180920.0280.0770.06320.797.2
1.94-2.136.90.04813.5114753167300.0230.0590.04826.797.6
2.13-2.387.10.04115108051152410.0190.0510.04132.498.1
2.38-2.756.90.03516.493350135190.0170.0440.03536.198.5
2.75-3.377.20.03215.982562115000.0150.0390.03243.998.9
3.37-4.766.90.02817.96127789350.0130.0330.02850.799.2
4.76-86.7046.80.02912.73432450190.0140.0360.02947.399.5

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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: 1.51→73.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.199 14403 9.9 %RANDOM
Rwork0.1656 ---
obs0.1689 130782 93.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.53 Å2 / Biso mean: 19.199 Å2 / Biso min: 6.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20.22 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.51→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8331 0 112 1114 9557
Biso mean--19.52 29.23 -
Num. residues----1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128908
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.64912168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22751087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.823.723470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.931151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8691531
X-RAY DIFFRACTIONr_chiral_restr0.1240.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027075
LS refinement shellResolution: 1.51→1.545 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.25 656 -
Rwork0.206 5693 -
obs--55.67 %

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