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

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Basic information

Entry
Database: PDB / ID: 5msb
TitleCrystal structure of human carbonic anhydrase isozyme XII with 2,3,5,6-tetrafluoro-4[(2-hydroxyethyl)sulfonyl]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 / 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-V13 / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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
DepositionJan 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 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 1.2Jan 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 / _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 1.3Oct 23, 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)121,75919
Polymers119,6694
Non-polymers2,08915
Water19,4921082
1
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,93210
Polymers59,8352
Non-polymers1,0988
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)60,8269
Polymers59,8352
Non-polymers9927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.104, 74.133, 91.587
Angle α, β, γ (deg.)90.000, 108.880, 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 , 5 types, 1097 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Fragment: 2,3,5,6-tetrafluoro-4[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Fragment: Zn / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-V13 / 2,3,5,6-tetrafluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 337.268 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7F4NO5S2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Fragment: EDO / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40 %
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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→74.133 Å / Num. all: 237650 / Num. obs: 237650 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Rsym value: 0.056 / Net I/av σ(I): 3.971 / Net I/σ(I): 14.2 / Num. measured all: 1615851
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.3-1.376.70.3981.9199.2
1.37-1.456.70.2732.6199.3
1.45-1.556.80.183.9199.3
1.55-1.686.70.125.3199.3
1.68-1.846.70.0856.4199.5
1.84-2.066.90.0638199.6
2.06-2.3770.0558.4199.6
2.37-2.9170.059.1199.6
2.91-4.1170.0449.2199.6
4.11-74.1336.70.0447.8199.5

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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

5ll9


Resolution: 1.3→72.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU R Cruickshank DPI: 0.0562 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.197 23661 10 %RANDOM
Rwork0.1489 ---
obs0.1537 213960 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 147.82 Å2 / Biso mean: 21.564 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.25 Å2
2--0.95 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.3→72.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8379 0 135 1082 9596
Biso mean--25.69 30.28 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.029007
X-RAY DIFFRACTIONr_angle_refined_deg2.1831.95512306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50651091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95724.768453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.964151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4531532
X-RAY DIFFRACTIONr_chiral_restr0.1470.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217114
X-RAY DIFFRACTIONr_rigid_bond_restr7.83839007
X-RAY DIFFRACTIONr_sphericity_free23.40951086
X-RAY DIFFRACTIONr_sphericity_bonded19.26558737
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 1796 -
Rwork0.194 15634 -
all-17430 -
obs--99.15 %

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