[English] 日本語
Yorodumi
- PDB-8dyq: Crystal structure of Neisseria gonorrhoeae carbonic anhydrase wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dyq
TitleCrystal structure of Neisseria gonorrhoeae carbonic anhydrase with Acetazolamide
ComponentsCarbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / Neisseria gonorrhoeae / Acetazolamide
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / periplasmic space / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / 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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsMarapaka, A.K. / Das, C. / Flaherty, D.P. / Yadav, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148523 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Structural Characterization of Thiadiazolesulfonamide Inhibitors Bound to Neisseria gonorrhoeae alpha-Carbonic Anhydrase.
Authors: Marapaka, A.K. / Nocentini, A. / Youse, M.S. / An, W. / Holly, K.J. / Das, C. / Yadav, R. / Seleem, M.N. / Supuran, C.T. / Flaherty, D.P.
History
DepositionAug 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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
A: Carbonic anhydrase
C: Carbonic anhydrase
E: Carbonic anhydrase
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,18220
Polymers109,2634
Non-polymers1,91916
Water66737
1
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6994
Polymers27,3161
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7965
Polymers27,3161
Non-polymers4804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9887
Polymers27,3161
Non-polymers6726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6994
Polymers27,3161
Non-polymers3843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.969, 122.592, 78.354
Angle α, β, γ (deg.)90.000, 117.210, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Carbonic anhydrase / Carbonate dehydratase


Mass: 27315.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: cah / Production host: Escherichia coli (E. coli) / References: UniProt: Q50940, carbonic anhydrase
#2: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M NH4H2PO4, 2.2 M (NH4)2SO4 / PH range: 6-8

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 60187 / % possible obs: 91.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.06 / Rrim(I) all: 0.152 / Χ2: 0.836 / Net I/σ(I): 4.1 / Num. measured all: 350505
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.233.50.38242580.7610.2080.4370.57265.1
2.23-2.324.10.36148830.8130.1810.4060.63874.4
2.32-2.424.70.33954890.8390.1620.3780.61184.2
2.42-2.555.20.31161220.8840.1430.3430.60493.4
2.55-2.716.20.28564820.9290.1220.3110.64499.3
2.71-2.926.40.23365860.9480.0990.2540.689100
2.92-3.216.60.1865400.9650.0750.1950.815100
3.21-3.686.70.12865700.9790.0530.1381.043100
3.68-4.636.80.09765850.9860.040.1051.153100
4.63-106.60.0866720.9910.0340.0871.08100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.509
Highest resolutionLowest resolution
Rotation46.03 Å2.37 Å

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREP11.9.02; 28.02.2022phasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KOP

1kop


Resolution: 2.15→46.02 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.823 / SU B: 8.399 / SU ML: 0.217 / SU R Cruickshank DPI: 0.2892 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3141 2850 4.7 %RANDOM
Rwork0.259 ---
obs0.2616 57306 91.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.38 Å2 / Biso mean: 26.365 Å2 / Biso min: 2.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.15→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 96 37 7094
Biso mean--35 17.49 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127253
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166361
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6589901
X-RAY DIFFRACTIONr_angle_other_deg0.5121.55314877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2755890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.0881035
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.223101148
X-RAY DIFFRACTIONr_chiral_restr0.0670.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 151 -
Rwork0.298 2906 -
all-3057 -
obs--63.36 %

+
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