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- PDB-6t5q: Human Carbonic anhydrase XII bound by 3,5-diphenylbenzenesulfonamide -

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Basic information

Entry
Database: PDB / ID: 6t5q
TitleHuman Carbonic anhydrase XII bound by 3,5-diphenylbenzenesulfonamide
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
3,5-diphenylbenzenesulfonamide / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Biophys.J. / Year: 2020
Title: Isoform-Selective Enzyme Inhibitors by Exploring Pocket Size According to the Lock-and-Key Principle.
Authors: Dudutiene, V. / Zubriene, A. / Kairys, V. / Smirnov, A. / Smirnoviene, J. / Leitans, J. / Kazaks, A. / Tars, K. / Manakova, L. / Grazulis, S. / Matulis, D.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)120,98313
Polymers119,6694
Non-polymers1,3149
Water9,116506
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7088
Polymers59,8352
Non-polymers8746
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)60,2755
Polymers59,8352
Non-polymers4403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.017, 68.832, 97.899
Angle α, β, γ (deg.)90.000, 112.570, 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta / 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-MKQ / 3,5-diphenylbenzenesulfonamide


Mass: 309.382 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H15NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / 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 Å3/Da / Density % sol: 38.57 %
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: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→90.404 Å / Num. all: 85968 / Num. obs: 85968 / % possible obs: 98.1 % / Redundancy: 6.9 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Rsym value: 0.074 / Net I/av σ(I): 6.6 / Net I/σ(I): 13.4 / Num. measured all: 596360
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
1.8-1.96.80.3821.983751123660.170.4460.3824.597
1.9-2.017.10.242.982581117120.1040.280.246.697.3
2.01-2.157.10.1684.278652110790.0730.1950.1688.897.7
2.15-2.326.70.1275.568649103180.0580.1510.12710.298.1
2.32-2.557.20.1036.86860095620.0440.1190.10312.798.3
2.55-2.8570.0828.36109186860.0360.0960.08215.698.6
2.85-3.296.90.0689.85299877100.030.0790.06820.199
3.29-4.027.10.055124642765570.0240.0630.05527.199.3
4.02-5.696.80.04713.43450750990.0210.0550.04729.199.5
5.69-90.4046.60.0489.21910428790.0210.0550.04827.399.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT2

4ht2


Resolution: 1.8→54.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.137
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 8557 10 %RANDOM
Rwork0.1742 ---
obs0.1783 77363 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 24.751 Å2 / Biso min: 9.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.23 Å2
2--0.93 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.8→54.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8250 0 78 506 8834
Biso mean--36.27 31.09 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128601
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.64411731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2951042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65423.575442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.571151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0861528
X-RAY DIFFRACTIONr_chiral_restr0.1230.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026800
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 605 -
Rwork0.209 5644 -
all-6249 -
obs--96.6 %

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