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- PDB-7pp9: Three dimensional structure of human carbonic anhydrase XII in co... -

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Basic information

Entry
Database: PDB / ID: 7pp9
TitleThree dimensional structure of human carbonic anhydrase XII in complex with sulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / CA XII / CA 12 / carbonic anhydrase XII / carbonic anhydrase 12
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-7VZ / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsLeitans, J. / Tars, K. / Dvinskis, E.
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 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 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)121,14612
Polymers119,4294
Non-polymers1,7178
Water13,223734
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5736
Polymers59,7142
Non-polymers8594
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)60,5736
Polymers59,7142
Non-polymers8594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.822, 74.862, 76.439
Angle α, β, γ (deg.)90.000, 105.460, 90.020
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-7VZ / methyl 2-chloranyl-4-cyclohexylsulfanyl-5-sulfamoyl-benzoate


Mass: 363.880 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H18ClNO4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.15 Å3/Da / Density % sol: 42.8 % / Description: two dimers
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 19, 2017 / Details: MULTILAYER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→74.86 Å / Num. obs: 54029 / % possible obs: 94.7 % / Redundancy: 5.23 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.6
Reflection shellResolution: 2.34→2.39 Å / Redundancy: 3.58 % / Rmerge(I) obs: 0.3475 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 3077 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QNL

6qnl


Resolution: 2.34→74.86 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.868 / SU B: 9.914 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.823 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 2085 5.1 %RANDOM
Rwork0.1607 ---
obs0.1652 38566 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.4 Å2 / Biso mean: 17.057 Å2 / Biso min: 2.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20.01 Å2-0.2 Å2
2--1.47 Å2-0.03 Å2
3----0.75 Å2
Refinement stepCycle: final / Resolution: 2.34→74.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8316 0 92 734 9142
Biso mean--22.82 21.44 -
Num. residues----1040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138656
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177689
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.65611795
X-RAY DIFFRACTIONr_angle_other_deg1.3061.58517753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.27651028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7723.521463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.353151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8011532
X-RAY DIFFRACTIONr_chiral_restr0.0780.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022036
LS refinement shellResolution: 2.341→2.402 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 151 -
Rwork0.237 2557 -
all-2708 -
obs--87.87 %

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