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

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Basic information

Entry
Database: PDB / ID: 6xzx
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 / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
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-O5H / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,6406
Polymers57,8122
Non-polymers8284
Water10,899605
1
A: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3203
Polymers28,9061
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3203
Polymers28,9061
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.841, 70.985, 120.802
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-O5H / 1-[2-[(phenylmethyl)amino]ethyl]-3-(3-sulfamoylphenyl)urea


Mass: 348.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N4O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
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: 1.55→62.85 Å / Num. obs: 79244 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.025 / Net I/σ(I): 12.2
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.793 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5757 / Rpim(I) all: 0.526 / % possible all: 100

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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: 1.55→60.401 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / Phase error: 28.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 3858 4.8 %Random
Rwork0.2002 ---
obs0.2013 78980 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.56 Å2
Refinement stepCycle: LAST / Resolution: 1.55→60.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 50 605 4666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824197
X-RAY DIFFRACTIONf_angle_d0.91095719
X-RAY DIFFRACTIONf_chiral_restr0.0598608
X-RAY DIFFRACTIONf_plane_restr0.0057746
X-RAY DIFFRACTIONf_dihedral_angle_d21.23251507

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