PDB-7oa1: Crystal structure of alfa carbonic anhydrase from Schistosoma man...

ID or keywords:

Entry

Database: PDB / ID: 7oa1

Title

Crystal structure of alfa carbonic anhydrase from Schistosoma mansoni with 4-(2-(3-(4-iodophenyl)ureido)ethyl)benzenesulfonamide

Components

Carbonic anhydrase

Keywords

LYASE / carbonic anhydrase / inhibitor / schistosoma mansoni

Function / homology

Function and homology information

carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / zinc ion binding / plasma membrane
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Angelil, A. / Ferraroni, M.

Citation

Journal: J.Med.Chem. / Year: 2021
Title: Structural Insights into Schistosoma mansoni Carbonic Anhydrase (SmCA) Inhibition by Selenoureido-Substituted Benzenesulfonamides.
Authors: Angeli, A. / Ferraroni, M. / Da'dara, A.A. / Selleri, S. / Pinteala, M. / Carta, F. / Skelly, P.J. / Supuran, C.T.

History

Deposition	Apr 18, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7oa1.cif.gz	145.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7oa1.ent.gz		Display	PDB format
PDBx/mmJSON format	7oa1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7oa1_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	7oa1_full_validation.pdf.gz	2.4 MB	Display
Data in XML	7oa1_validation.xml.gz	27.5 KB	Display
Data in CIF	7oa1_validation.cif.gz	38.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/7oa1 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oa1	HTTPS FTP

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Related structure data

Related structure data	6qqmSC 7bfaC 7bg5C 7bhhC 7bm4C 7nexC 7ng1C 7nwyC 7o2sC 7o48C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#49 - Jan 2004 Carbonic Anhydrase similarity (1)

Deposited unit

AAA: Carbonic anhydrase

BBB: Carbonic anhydrase

hetero molecules

74.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	103.500, 103.500, 133.290
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

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Protein , 1 types, 2 molecules AAABBB

#1: Protein	Carbonic anhydrase Mass: 35704.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A3Q0KSG2, carbonic anhydrase

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Sugars , 2 types, 6 molecules

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 317 molecules

#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-TKQ / 1-(4-iodophenyl)-3-[2-(4-sulfamoylphenyl)ethyl]urea Mass: 445.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₁₆IN₃O₃S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.38 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 6000, 0.1 M citrate pH 5.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→89.64 Å / Num. obs: 83597 / % possible obs: 99.4 % / Redundancy: 16 % / CC_1/2: 0.999 / R_merge(I) obs: 0.089 / R_rim(I) all: 0.092 / Net I/σ(I): 18.17
Reflection shell	Resolution: 1.75→1.79 Å / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 5809 / CC_1/2: 0.907 / R_rim(I) all: 0.557 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6qqm

6qqm

Resolution: 2→89.634 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.951 / SU B: 2.688 / SU ML: 0.076 / Cross valid method: NONE / ESU R: 0.128 / ESU R Free: 0.121
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1944	2818	5.006 %
R_work	0.1643	53474	-
all	0.166	-	-
obs	-	56292	99.963 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.416 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.295 Å²	0.148 Å²	0 Å²
2-	-	0.295 Å²	-0 Å²
3-	-	-	-0.958 Å²

Refinement step

Cycle: LAST / Resolution: 2→89.634 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4473	0	152	312	4937

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	4783
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4205
X-RAY DIFFRACTION	r_angle_refined_deg	1.865	1.673	6513
X-RAY DIFFRACTION	r_angle_other_deg	1.44	1.603	9779
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.692	5	564
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.649	22.101	257
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.833	15	745
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.973	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	647
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	5447
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1058
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	892
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	4303
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	2372
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	2236
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	284
X-RAY DIFFRACTION	r_metal_ion_refined	0.139	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.34	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.245	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.131	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.929	2.74	2230
X-RAY DIFFRACTION	r_mcbond_other	2.928	2.743	2231
X-RAY DIFFRACTION	r_mcangle_it	3.769	4.088	2784
X-RAY DIFFRACTION	r_mcangle_other	3.724	4.089	2784
X-RAY DIFFRACTION	r_scbond_it	5.315	3.316	2553
X-RAY DIFFRACTION	r_scbond_other	5.314	3.32	2554
X-RAY DIFFRACTION	r_scangle_it	7.839	4.807	3723
X-RAY DIFFRACTION	r_scangle_other	7.844	4.811	3724
X-RAY DIFFRACTION	r_lrange_it	7.889	33.924	5344
X-RAY DIFFRACTION	r_lrange_other	7.859	33.908	5342

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2-2.052	0.225	202	0.17	3899	0.173	4101	0.944	0.954	100	0.15
2.052-2.108	0.201	187	0.163	3843	0.165	4030	0.947	0.956	100	0.145
2.108-2.169	0.248	186	0.17	3700	0.173	3886	0.93	0.951	100	0.152
2.169-2.236	0.245	199	0.181	3609	0.184	3815	0.928	0.945	99.8165	0.164
2.236-2.309	0.203	175	0.173	3482	0.175	3670	0.954	0.955	99.6458	0.161
2.309-2.39	0.197	174	0.168	3364	0.169	3538	0.947	0.953	100	0.159
2.39-2.48	0.207	204	0.164	3248	0.167	3452	0.949	0.959	100	0.16
2.48-2.582	0.173	162	0.153	3158	0.154	3320	0.957	0.963	100	0.152
2.582-2.696	0.206	170	0.166	3000	0.168	3170	0.949	0.956	100	0.169
2.696-2.828	0.214	135	0.169	2918	0.172	3053	0.949	0.954	100	0.175
2.828-2.981	0.215	150	0.172	2765	0.175	2915	0.943	0.954	100	0.182
2.981-3.161	0.215	137	0.177	2613	0.179	2750	0.945	0.956	100	0.192
3.161-3.379	0.205	135	0.177	2469	0.179	2604	0.947	0.96	100	0.195
3.379-3.649	0.21	127	0.178	2286	0.18	2413	0.952	0.961	100	0.197
3.649-3.997	0.156	89	0.155	2152	0.155	2241	0.975	0.973	100	0.178
3.997-4.468	0.144	97	0.13	1952	0.131	2049	0.977	0.977	100	0.158
4.468-5.157	0.166	93	0.131	1703	0.132	1796	0.974	0.98	100	0.165
5.157-6.31	0.176	86	0.154	1452	0.155	1538	0.977	0.978	100	0.192
6.31-8.902	0.202	72	0.167	1163	0.169	1235	0.966	0.972	100	0.212
8.902-89.634	0.184	38	0.23	684	0.227	723	0.956	0.942	99.8617	0.288

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Protein , 1 types, 2 molecules AAABBB

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