[English] 日本語
Yorodumi
- PDB-7pri: Carbonic Anhydrase from Schistosoma Mansoni in complex with clorsulon -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pri
TitleCarbonic Anhydrase from Schistosoma Mansoni in complex with clorsulon
ComponentsCarbonic anhydrase
KeywordsLYASE / inhibitor / sulfonamide / schistosoma / schistosomiasis
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / 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
Chem-7TI / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies.
Authors: Ferraroni, M. / Angeli, A. / Carradori, S. / Supuran, C.T.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Carbonic anhydrase
BBB: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,31012
Polymers64,2202
Non-polymers2,09010
Water6,738374
1
AAA: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9995
Polymers32,1101
Non-polymers8884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3127
Polymers32,1101
Non-polymers1,2026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.800, 103.800, 132.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein / Sugars , 2 types, 7 molecules AAABBB

#1: Protein Carbonic anhydrase


Mass: 32110.084 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
#3: 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
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

-
Non-polymers , 4 types, 379 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-7TI / 4-azanyl-6-[1,2,2-tris(chloranyl)ethenyl]benzene-1,3-disulfonamide / clorsulon


Mass: 380.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8Cl3N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 6000, 0.1 M citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9719 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9719 Å / Relative weight: 1
ReflectionResolution: 1.68→89.9 Å / Num. obs: 94460 / % possible obs: 99.7 % / Redundancy: 17.26 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.099 / Net I/σ(I): 27.43
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 8.93 % / Rmerge(I) obs: 1.18 / Num. unique obs: 6740 / CC1/2: 0.706 / Rrim(I) all: 1 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QQM

6qqm


Resolution: 1.679→89.893 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.163 / SU B: 1.562 / SU ML: 0.051 / Average fsc free: 0.9429 / Average fsc work: 0.9495 / Cross valid method: NONE / ESU R: 0.076 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1951 4543 4.81 %
Rwork0.1669 89907 -
all0.168 --
obs-94450 99.685 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20.013 Å20 Å2
2--0.025 Å2-0 Å2
3----0.082 Å2
Refinement stepCycle: LAST / Resolution: 1.679→89.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 118 374 4986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174314
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.6716480
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5959924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5445556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77121.985262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69115758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.111532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
X-RAY DIFFRACTIONr_nbd_refined0.2070.2826
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24183
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22341
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.28
X-RAY DIFFRACTIONr_nbd_other0.2050.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.217
X-RAY DIFFRACTIONr_mcbond_it2.1722.1612218
X-RAY DIFFRACTIONr_mcbond_other2.1582.1582216
X-RAY DIFFRACTIONr_mcangle_it2.9983.2312772
X-RAY DIFFRACTIONr_mcangle_other2.9923.232770
X-RAY DIFFRACTIONr_scbond_it3.472.552531
X-RAY DIFFRACTIONr_scbond_other3.372.5412526
X-RAY DIFFRACTIONr_scangle_it5.2333.73706
X-RAY DIFFRACTIONr_scangle_other5.0893.693701
X-RAY DIFFRACTIONr_lrange_it6.77426.5245237
X-RAY DIFFRACTIONr_lrange_other6.64126.5015234
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.679-1.7230.2643470.25963720.2669260.8720.87497.01130.244
1.723-1.770.2523160.21563630.21767500.9120.91698.94820.194
1.77-1.8210.223140.18962830.1966020.9270.93699.92430.164
1.821-1.8770.1922680.17961100.17963780.9460.9481000.152
1.877-1.9390.2042880.17559120.17762000.9420.9491000.147
1.939-2.0070.1953340.16456910.16660250.9550.961000.14
2.007-2.0830.1973080.17754790.17857870.950.9541000.152
2.083-2.1680.212640.16753240.16955880.9450.9581000.146
2.168-2.2640.1912410.16651130.16853540.9520.9591000.146
2.264-2.3740.1942320.15649020.15751340.9580.9661000.14
2.374-2.5030.2032480.15746380.15948860.9510.9631000.145
2.503-2.6540.1732360.15744090.15846450.9640.9641000.148
2.654-2.8380.1882370.16141180.16243550.9540.9611000.155
2.838-3.0650.1981810.16838920.16940730.9530.9631000.166
3.065-3.3570.1941700.17635960.17737660.9590.9611000.18
3.357-3.7520.1831560.16332580.16434140.9640.971000.171
3.752-4.3310.1521630.13628770.13630400.9740.9791000.151
4.331-5.3020.1441040.13724750.13725790.9830.9831000.159
5.302-7.4850.242900.18419550.18620450.9610.971000.208
7.485-89.8930.338460.20711400.21211890.8990.94699.74770.237

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more