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- PDB-6y00: crystal structure of human carbonic anhydrase I in complex with 4... -

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Basic information

Entry
Database: PDB / ID: 6y00
Titlecrystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide
ComponentsCarbonic anhydrase 1
KeywordsLYASE / Inhibitor / carbon dioxide / carbonic anhydrase
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / extracellular exosome / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-O5T / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsZanotti, G. / Majid, A. / Bozdag, M. / Angeli, A. / Carta, F. / Berto, P. / Supuran, C.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Benzylaminoethyureido-Tailed Benzenesulfonamides: Design, Synthesis, Kinetic and X-ray Investigations on Human Carbonic Anhydrases.
Authors: Ali, M. / Bozdag, M. / Farooq, U. / Angeli, A. / Carta, F. / Berto, P. / Zanotti, G. / Supuran, C.T.
History
DepositionFeb 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8306
Polymers57,8122
Non-polymers1,0174
Water13,259736
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4153
Polymers28,9061
Non-polymers5092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4153
Polymers28,9061
Non-polymers5092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.572, 71.384, 121.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Erythrocytes / References: UniProt: P00915, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-O5T / 1-[2-[(4-bromanyl-2-oxidanyl-phenyl)methylamino]ethyl]-3-(3-sulfamoylphenyl)urea


Mass: 443.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19BrN4O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9. Inhibitor: 150 mM NaCl, 10% DMSO, 50 mM Tris pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.37→61.5 Å / Num. obs: 114640 / % possible obs: 99.9 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Net I/σ(I): 14.6
Reflection shellResolution: 1.37→1.41 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1 / Num. unique obs: 8252 / Rpim(I) all: 0.522 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xze

6xze


Resolution: 1.37→60.699 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 28.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 5627 4.92 %random
Rwork0.1978 ---
obs0.1988 114319 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.33 Å2
Refinement stepCycle: LAST / Resolution: 1.37→60.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 54 736 4801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00574201
X-RAY DIFFRACTIONf_angle_d0.92875727
X-RAY DIFFRACTIONf_chiral_restr0.0795608
X-RAY DIFFRACTIONf_plane_restr0.0057746
X-RAY DIFFRACTIONf_dihedral_angle_d20.62851507

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