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- PDB-6qqm: Crystal structure of the alpha carbonic anhydrase from Schistosom... -

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Basic information

Entry
Database: PDB / ID: 6qqm
TitleCrystal structure of the alpha carbonic anhydrase from Schistosoma mansoni
ComponentsPutative carbonic anhydrase
KeywordsLYASE
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / zinc ion binding / plasma membrane
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
Carbonic anhydrase / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsFerraroni, M. / Angeli, A. / Supuran, C.T.
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.
#1: Journal: Commun Biol / Year: 2019
Title: Crystal structure and chemical inhibition of essential schistosome host-interactive virulence factor carbonic anhydrase SmCA.
Authors: Da'dara, A.A. / Angeli, A. / Ferraroni, M. / Supuran, C.T. / Skelly, P.J.
History
DepositionFeb 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2May 4, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative carbonic anhydrase
B: Putative carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,10210
Polymers68,9022
Non-polymers1,2008
Water7,008389
1
A: Putative carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1436
Polymers34,4511
Non-polymers6925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9594
Polymers34,4511
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.040, 103.040, 132.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative carbonic anhydrase


Mass: 34450.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_168730 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: G4VLX3, UniProt: A0A3Q0KSG2*PLUS, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Potassium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0399 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0399 Å / Relative weight: 1
ReflectionResolution: 1.7→89.24 Å / Num. obs: 89134 / % possible obs: 98.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.114 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.8112.4621.9281141610.6062.00992.5
1.81-1.9314.2230.932.53129250.8920.965100
1.93-2.0913.6580.455.5130490.9670.468100
2.09-2.2913.6840.2529.74116040.9870.261100
2.29-2.5514.0980.15715.39101790.9940.163100
2.55-2.9513.60.11320.4495120.9950.117100
2.95-3.6114.1660.0925.9579020.9970.094100
3.61-5.0913.4580.0828.6362090.9970.083100
5.09-39.613.1890.07528.9535930.9970.07999.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.606
Highest resolutionLowest resolution
Rotation39.6 Å3 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pxx

4pxx


Resolution: 1.75→39.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.909 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0885 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.092 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 4301 5.2 %RANDOM
Rwork0.17 ---
obs0.1718 78052 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 302.3 Å2 / Biso mean: 26.563 Å2 / Biso min: 11.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å2-0 Å2
2--0.29 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 1.75→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4464 0 70 389 4923
Biso mean--47.09 33.76 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194692
X-RAY DIFFRACTIONr_angle_refined_deg2.3831.9516393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5455567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33623.744227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79915740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5211530
X-RAY DIFFRACTIONr_chiral_restr0.1920.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213582
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 311 -
Rwork0.231 5672 -
all-5983 -
obs--99.98 %

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