[English] 日本語
Yorodumi
- PDB-9dsf: Cyanide-ligated Bordetella pertussis globin coupled sensor regula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dsf
TitleCyanide-ligated Bordetella pertussis globin coupled sensor regulatory domain S68A
ComponentsDiguanylate cyclase DosC
KeywordsSIGNALING PROTEIN / Cooperativity / Oxygen-sensing / Cyano ligand / Heme
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / oxygen binding / nucleotide binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Diguanylate cyclase DosC, globin sensor domain / : / DosC CZB-like middle domain / Globin-sensor domain / Protoglobin / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain ...Diguanylate cyclase DosC, globin sensor domain / : / DosC CZB-like middle domain / Globin-sensor domain / Protoglobin / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Globin/Protoglobin / Globin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Diguanylate cyclase DosC
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHoque, N.J. / Pope, S.R. / Boal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Cooperative Ligand Binding in a Bacterial Heme-Based Oxygen Sensor.
Authors: Hoque, N.J. / Pope, S.R. / Venkatakrishnan, V. / Olori, D.O. / Brady, N.A. / Patterson, D.C. / Anand, G.S. / Liu, Y. / Boal, A.K. / Weinert, E.E.
History
DepositionSep 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diguanylate cyclase DosC
B: Diguanylate cyclase DosC
C: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,45710
Polymers57,4383
Non-polymers2,0207
Water1,982110
1
A: Diguanylate cyclase DosC
hetero molecules

A: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5776
Polymers38,2922
Non-polymers1,2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5100 Å2
ΔGint-58 kcal/mol
Surface area13380 Å2
MethodPISA
2
B: Diguanylate cyclase DosC
C: Diguanylate cyclase DosC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6697
Polymers38,2922
Non-polymers1,3775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-55 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.958, 49.702, 67.994
Angle α, β, γ (deg.)90.00, 110.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21B-333-

HOH

-
Components

#1: Protein Diguanylate cyclase DosC / Direct oxygen-sensing cyclase


Mass: 19145.934 Da / Num. of mol.: 3 / Mutation: S68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria)
Strain: Tohama I / ATCC BAA-589 / NCTC 13251 / Gene: BP3507 / Plasmid: pET-20b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 Tuner plysS / References: UniProt: Q7VTL8, diguanylate cyclase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.48 % / Description: Plates, rods
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10 mM Tris, 0.2 M Calcium Acetate, 10% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2023
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→46.67 Å / Num. obs: 38802 / % possible obs: 99.48 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.73 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.026 / Net I/σ(I): 21.1
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3885 / CC1/2: 0.886 / Rpim(I) all: 0.21 / % possible all: 99.64

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000722data reduction
HKL-2000722data scaling
PHASER7.1.018phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→46.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.304 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23862 1896 4.9 %RANDOM
Rwork0.20704 ---
obs0.20855 36907 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.359 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-0 Å2-0.92 Å2
2--1.13 Å20 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.85→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 141 110 3898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153567
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.7025331
X-RAY DIFFRACTIONr_angle_other_deg1.1691.6038152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8575464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.2820.909198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8715588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2631530
X-RAY DIFFRACTIONr_chiral_restr0.0490.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02875
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8132.8691868
X-RAY DIFFRACTIONr_mcbond_other0.8132.8681866
X-RAY DIFFRACTIONr_mcangle_it1.4194.2982326
X-RAY DIFFRACTIONr_mcangle_other1.4184.2992327
X-RAY DIFFRACTIONr_scbond_it0.8492.9792023
X-RAY DIFFRACTIONr_scbond_other0.8422.9792017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4484.4123006
X-RAY DIFFRACTIONr_long_range_B_refined2.7433.4314585
X-RAY DIFFRACTIONr_long_range_B_other2.71133.414577
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 133 -
Rwork0.256 2678 -
obs--99.01 %

+
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