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- PDB-5msa: Crystal structure of human carbonic anhydrase isozyme XII with 2,... -

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Basic information

Entry
Database: PDB / ID: 5msa
TitleCrystal structure of human carbonic anhydrase isozyme XII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
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 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-3TV / CITRIC ACID / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: To be published
Title: Crystal structure of human carbonic anhydrase isozyme XII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
Authors: Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D. / Dudutiene, V.
History
DepositionJan 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: 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 / 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 / _diffrn_radiation_wavelength.wavelength / _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)122,89031
Polymers119,6694
Non-polymers3,22027
Water25,9781442
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,47317
Polymers59,8352
Non-polymers1,63815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Carbonic anhydrase 12
D: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,41714
Polymers59,8352
Non-polymers1,58212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.170, 74.157, 91.559
Angle α, β, γ (deg.)90.000, 108.850, 90.000
Int Tables number4
Space group name H-MP1211

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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 BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O43570, carbonic anhydrase

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Non-polymers , 6 types, 1469 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Fragment: 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-3TV / 2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide


Mass: 303.297 Da / Num. of mol.: 4 / Fragment: Zn / Source method: obtained synthetically / Formula: C9H9F4NO2S2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Fragment: CITRATE / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Fragment: DI(HYDROXYETHYL)ETHER / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1442 / 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: 2.07 Å3/Da / Density % sol: 40.3 %
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: P14 (MX2) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / 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: 1.2→73.032 Å / Num. all: 294981 / Num. obs: 294981 / % possible obs: 97.2 % / Redundancy: 6.9 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Rsym value: 0.057 / Net I/av σ(I): 2.903 / Net I/σ(I): 19.9 / Num. measured all: 2029753
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.2-1.266.60.1953.7194.4
1.26-1.346.90.1475195.8
1.34-1.436.90.1076.8196.4
1.43-1.556.90.0769.1196.9
1.55-1.76.80.05811.3198
1.7-1.970.04812.1197.9
1.9-2.197.10.04213.1199.1
2.19-2.6870.04112.9199.2
2.68-3.7970.0516.6199.8
3.79-73.0326.70.0695.7199.6

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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: 5LL9
Resolution: 1.2→67.64 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU R Cruickshank DPI: 0.0437 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.044
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 29410 10 %RANDOM
Rwork0.1408 ---
obs0.1445 265539 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 302.94 Å2 / Biso mean: 19.575 Å2 / Biso min: 4.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.29 Å2
2--0.22 Å20 Å2
3---0.12 Å2
Refinement stepCycle: final / Resolution: 1.2→67.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 245 1442 10083
Biso mean--27.78 30.88 -
Num. residues----1045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.029299
X-RAY DIFFRACTIONr_angle_refined_deg2.2251.96712731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38651148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22624.698447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.559151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.631533
X-RAY DIFFRACTIONr_chiral_restr0.1550.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217413
X-RAY DIFFRACTIONr_rigid_bond_restr8.80339299
X-RAY DIFFRACTIONr_sphericity_free30.6251446
X-RAY DIFFRACTIONr_sphericity_bonded24.18459010
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 2082 -
Rwork0.165 18930 -
all-21012 -
obs--93.65 %

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