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- PDB-5llp: Crystal structure of human carbonic anhydrase isozyme XII with 3-... -

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Basic information

Entry
Database: PDB / ID: 5llp
TitleCrystal structure of human carbonic anhydrase isozyme XII with 3-[(1S)-1,2,3,4-Tetrahydronapthalen-1-ylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor comple
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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-6Z9 / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: PeerJ / Year: 2018
Title: Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding.
Authors: Smirnov, A. / Zubriene, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)121,78912
Polymers119,6694
Non-polymers2,1208
Water21,3301184
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8946
Polymers59,8352
Non-polymers1,0604
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)60,8946
Polymers59,8352
Non-polymers1,0604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.488, 74.288, 91.658
Angle α, β, γ (deg.)90.000, 108.970, 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 XII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): rosetta / References: UniProt: O43570, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Fragment: 3-[(1S)-1,2,3,4-Tetrahydronapthalen-1-ylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-6Z9 / 3-[(1S)-1,2,3,4-Tetrahydronapthalen-1-ylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 464.479 Da / Num. of mol.: 4 / Fragment: Zn / Source method: obtained synthetically / Formula: C18H19F3N2O5S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1184 / Source method: isolated from a natural source / Formula: H2O
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: 40.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.2M ammonium sulfate and 26% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.48→73.28 Å / Num. obs: 160218 / % possible obs: 98.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 12.282 Å2 / Rsym value: 0.062 / Net I/av σ(I): 5.961 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.48-1.566.90.2562.4196.6
1.56-1.656.70.1773.6197.4
1.65-1.776.90.1255.2197.7
1.77-1.917.10.0917197.6
1.91-2.097.10.0718.5198.6
2.09-2.3470.0629.5199
2.34-2.770.05510.5198.8
2.7-3.3170.05210.3199.6
3.31-4.686.60.04511.5199.6
4.68-73.2870.0457.9199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JD0

1jd0


Resolution: 1.48→73.28 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.0779 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 15901 9.9 %RANDOM
Rwork0.1635 ---
obs0.167 144263 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 15.619 Å2 / Biso min: 3.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.11 Å2
2--0.22 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.48→73.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8365 0 154 1184 9703
Biso mean--22.39 25.57 -
Num. residues----1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.029062
X-RAY DIFFRACTIONr_angle_refined_deg2.3391.96212409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48751098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21424.578450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.348151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0361535
X-RAY DIFFRACTIONr_chiral_restr0.160.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217192
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 1171 -
Rwork0.18 10373 -
all-11544 -
obs--95.93 %

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