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- PDB-6g7a: Crystal structure of human carbonic anhydrase isozyme XII 2-(benz... -

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Basic information

Entry
Database: PDB / ID: 6g7a
TitleCrystal structure of human carbonic anhydrase isozyme XII 2-(benzylamino)-4-chloro-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
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 / 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
Chem-EOQ / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Kisonaite, M. / Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionApr 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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.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

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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)122,21124
Polymers119,6694
Non-polymers2,54220
Water24,4281356
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,98110
Polymers59,8352
Non-polymers1,1478
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)61,23014
Polymers59,8352
Non-polymers1,39512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.296, 73.925, 91.217
Angle α, β, γ (deg.)90.000, 108.920, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimers:

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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 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
Fragment: 2-(benzylamino)-4-chloro-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-EOQ / 4-chloranyl-~{N}-(2-hydroxyethyl)-2-[(phenylmethyl)amino]-5-sulfamoyl-benzamide


Mass: 383.850 Da / Num. of mol.: 4 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C16H18ClN3O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1356 / 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: 2.06 Å3/Da / Density % sol: 39.9 %
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
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.42→86.29 Å / Num. obs: 173178 / % possible obs: 94.9 % / Redundancy: 6.8 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Rsym value: 0.036 / Net I/av σ(I): 10.568 / Net I/σ(I): 24.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.42-1.560.1864.1205030.0890.2270.18677.2
1.5-1.5970.1425.30.0640.1720.14296.5
1.59-1.76.70.1047.10.0490.1290.10496.8
1.7-1.837.10.0749.70.0350.0930.07497.5
1.83-2.016.70.05213.30.0260.0670.05297.9
2.01-2.257.20.0416.70.0190.0510.0498.3
2.25-2.596.80.03418.60.0170.0450.03498.7
2.59-3.187.20.02820.50.0140.0370.02899.4
3.18-4.496.80.02420.90.0120.030.02499.5
4.49-86.296.80.02315.50.0120.030.02399.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LL9

5ll9


Resolution: 1.42→73.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.0681 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 17232 10 %RANDOM
Rwork0.1525 ---
obs0.1558 173152 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 83.58 Å2 / Biso mean: 17.0153 Å2 / Biso min: 5.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.2 Å2
2--0.16 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.42→73.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8408 0 152 1356 9916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0199130
X-RAY DIFFRACTIONr_angle_refined_deg2.3321.95912447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90451103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72524.583456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.138151426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8181537
X-RAY DIFFRACTIONr_chiral_restr0.1670.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217250
X-RAY DIFFRACTIONr_mcbond_it1.7541.3514343
X-RAY DIFFRACTIONr_mcangle_it2.522.0215469
X-RAY DIFFRACTIONr_scbond_it3.0811.6254787
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 789 -
Rwork0.184 7390 -
all-8179 -
obs--60.68 %

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