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- PDB-5ohh: Crystal structure of human carbonic anhydrase isozyme XIII with 2... -

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Basic information

Entry
Database: PDB / ID: 5ohh
TitleCrystal structure of human carbonic anhydrase isozyme XIII with 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide
ComponentsCarbonic anhydrase 13
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / cytosol / cytoplasm
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-5DU / ACETATE ION / AZIDE ION / CITRIC ACID / PERCHLORATE ION / DI(HYDROXYETHYL)ETHER / Carbonic anhydrase 13
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: To be published
Title: Crystal structure of human carbonic anhydrase isozyme XIII with 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide
Authors: Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Carbonic anhydrase 13
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,61423
Polymers59,2272
Non-polymers2,38721
Water12,592699
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-55 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.501, 57.419, 159.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Carbonic anhydrase 13 / Carbonate dehydratase XIII / Carbonic anhydrase XIII / CA-XIII


Mass: 29613.318 Da / Num. of mol.: 2 / Fragment: human carbonic anhydrase XIII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8N1Q1, carbonic anhydrase

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Non-polymers , 10 types, 720 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#6: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-LCP / PERCHLORATE ION


Mass: 99.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: ClO4
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-5DU / 2-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)sulfanyl]benzenesulfonamide


Mass: 418.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17F3N2O3S2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.19 Å3/Da / Density % sol: 43.83 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: evaporation / pH: 5
Details: Crystallization buffer: 0.1M sodium citrate (pH 5.5), 0.1M sodium acetate (pH 4.5) 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: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.42→56.501 Å / Num. all: 99072 / Num. obs: 99072 / % possible obs: 100 % / Redundancy: 13.2 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Rsym value: 0.057 / Net I/av σ(I): 9.125 / Net I/σ(I): 26.5 / Num. measured all: 1305377
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value
1.42-1.512.60.4091.90.1250.4450.409
1.5-1.5913.50.2812.70.0820.3050.281
1.59-1.713.20.2043.80.0610.2230.204
1.7-1.8312.90.1365.60.0410.1490.136
1.83-2.0113.60.098.20.0260.0980.09
2.01-2.2512.90.06411.20.020.0710.064
2.25-2.5913.90.0513.80.0150.0560.05
2.59-3.1813.10.03916.50.0120.0440.039
3.18-4.4913.50.0319.50.0090.0330.03
4.49-56.50112.30.02917.60.0090.0330.029

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLN

5lln


Resolution: 1.42→54.04 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1811 / WRfactor Rwork: 0.1526 / FOM work R set: 0.9068 / SU R Cruickshank DPI: 0.0632 / SU Rfree: 0.0654 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 9977 10.1 %RANDOM
Rwork0.1565 ---
obs0.1593 89004 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.52 Å2 / Biso mean: 15.612 Å2 / Biso min: 4.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 1.42→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 150 699 4964
Biso mean--36.59 25.26 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.024584
X-RAY DIFFRACTIONr_angle_refined_deg2.4811.9736251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69824.293205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85315726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5131520
X-RAY DIFFRACTIONr_chiral_restr0.1620.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213582
LS refinement shellResolution: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 707 -
Rwork0.193 6522 -
all-7229 -
obs--100 %

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