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- PDB-4ht2: Crystal structure of human carbonic anhydrase isozyme XII with th... -

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Basic information

Entry
Database: PDB / ID: 4ht2
TitleCrystal structure of human carbonic anhydrase isozyme XII with the inhibitor.
ComponentsCarbonic anhydrase 12
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex / catalytic activity / carbon-oxygen lyase activity / carbonate dehydratase activity / Membrane
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 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
DI(HYDROXYETHYL)ETHER / Chem-V50 / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: 4-Substituted-2,3,5,6-tetrafluorobenzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, XII, and XIII.
Authors: Dudutiene, V. / Zubriene, A. / Smirnov, A. / Gylyte, J. / Timm, D. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)122,46327
Polymers119,6694
Non-polymers2,79423
Water27,0951504
1
A: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6427
Polymers29,9171
Non-polymers7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7679
Polymers29,9171
Non-polymers8498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4124
Polymers29,9171
Non-polymers4953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6427
Polymers29,9171
Non-polymers7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.709, 67.261, 80.689
Angle α, β, γ (deg.)81.78, 84.01, 86.48
Int Tables number1
Space group name H-MP1

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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 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): Rosetta(DE3) / References: UniProt: O43570, carbonic anhydrase

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Non-polymers , 5 types, 1527 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-V50 / 4-[(4,6-dimethylpyrimidin-2-yl)thio]-2,3,5,6-tetrafluorobenzenesulfonamide


Mass: 367.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H9F4N3O2S2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1504 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M ammonium citrate with pH 5.0 and 16% of PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2011 / Details: Mirror Bent, vertically focussing
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.45→27.164 Å / Num. obs: 166179 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.45-1.5340.2193.494703239050.21995.6
1.53-1.6240.1484.990400228170.14896.2
1.62-1.7340.1066.784748213910.10696.5
1.73-1.8740.0728.879680201330.07296.9
1.87-2.0540.04812.473179184840.04897.3
2.05-2.2940.03616.266575168200.03697.7
2.29-2.6540.03117.959016149050.03198.1
2.65-3.2440.02515.449986126320.02598.5
3.24-4.5940.02218.53870597840.02298.9
4.59-27.163.80.02215.71998753080.02297.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.3.16data scaling
PDB_EXTRACT3.006data extraction
DNAdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JD0

1jd0


Resolution: 1.45→26.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.9 / SU R Cruickshank DPI: 0.071 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 16455 9.9 %RANDOM
Rwork0.15 ---
all0.154 166179 --
obs0.154 166177 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.63 Å2 / Biso mean: 12.981 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20.05 Å20.02 Å2
2---0.1 Å20.49 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.45→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8392 0 165 1504 10061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0219207
X-RAY DIFFRACTIONr_angle_refined_deg2.4621.9612582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37351120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67124.683457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.132151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1811534
X-RAY DIFFRACTIONr_chiral_restr0.20.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.027325
X-RAY DIFFRACTIONr_nbd_refined0.2280.24473
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26186
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.21176
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.2165
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.2126
X-RAY DIFFRACTIONr_mcbond_it1.4321.55480
X-RAY DIFFRACTIONr_mcangle_it2.21428927
X-RAY DIFFRACTIONr_scbond_it3.12933727
X-RAY DIFFRACTIONr_scangle_it4.4484.53655
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 1155 -
Rwork0.197 10865 -
all-12020 -
obs-10865 95.55 %

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