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- PDB-6qng: Three dimensional structure of human carbonic anhydrase XII in co... -

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Basic information

Entry
Database: PDB / ID: 6qng
TitleThree dimensional structure of human carbonic anhydrase XII in complex with benzenesulfonamide
ComponentsCarbonic anhydrase 12
KeywordsLYASE
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-J95 / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsDvinskis, E. / Leitans, J. / Tars, K.
CitationJournal: To Be Published
Title: Three dimensional structure of human carbonic anhydrase XII in complex with benzenesulfonamide
Authors: Dvinskis, E. / Leitans, J. / Tars, K.
History
DepositionFeb 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / 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.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 1.2Nov 13, 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)121,24212
Polymers119,4294
Non-polymers1,8138
Water14,898827
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6216
Polymers59,7142
Non-polymers9074
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)60,6216
Polymers59,7142
Non-polymers9074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.930, 66.050, 80.950
Angle α, β, γ (deg.)82.09, 84.41, 86.17
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-J95 / ~{N}-butyl-4-chloranyl-2-(cyclohexylamino)-5-sulfamoyl-benzamide


Mass: 387.925 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H26ClN3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
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 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→65.33 Å / Num. obs: 89465 / % possible obs: 80.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.16 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 5.6
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2 / Num. unique obs: 12267 / % possible all: 75.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JD0

1jd0


Resolution: 1.67→65.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.976 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24973 4450 5 %RANDOM
Rwork0.19239 ---
obs0.1952 85012 80.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.337 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.8 Å20.47 Å2
2--0.95 Å21.28 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.67→65.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8340 0 104 828 9272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138702
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177521
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.65811851
X-RAY DIFFRACTIONr_angle_other_deg1.3471.58517580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70151032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6423.576467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.949151342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.11532
X-RAY DIFFRACTIONr_chiral_restr0.0910.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021811
X-RAY DIFFRACTIONr_mcbond_it1.551.7044152
X-RAY DIFFRACTIONr_mcbond_other1.5491.7044151
X-RAY DIFFRACTIONr_mcangle_it2.4362.5475170
X-RAY DIFFRACTIONr_mcangle_other2.4362.5485171
X-RAY DIFFRACTIONr_scbond_it2.0271.9254550
X-RAY DIFFRACTIONr_scbond_other2.0271.9254551
X-RAY DIFFRACTIONr_scangle_other3.1952.7986680
X-RAY DIFFRACTIONr_long_range_B_refined5.00720.7559753
X-RAY DIFFRACTIONr_long_range_B_other4.920.4559602
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 284 -
Rwork0.391 5217 -
obs--66.95 %

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