[English] 日本語
Yorodumi
- PDB-8k3b: The Pseudomonas aeruginosa RccR protein complexed with KDPG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k3b
TitleThe Pseudomonas aeruginosa RccR protein complexed with KDPG
ComponentsMurR/RpiR family transcriptional regulator
KeywordsGENE REGULATION / complex
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / LacI-type HTH domain signature. / SIS domain / SIS domain profile. / SIS domain superfamily ...Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / LacI-type HTH domain signature. / SIS domain / SIS domain profile. / SIS domain superfamily / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
2-keto 3 deoxy 6 phospho gluconate / HTH-type transcriptional regulator YbbH
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, Y.J. / Wu, Z.W. / Ji, Q.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277078 China
CitationJournal: To Be Published
Title: A KDPG sensor RccR governs Pseudomonas aeruginosa carbon metabolism and aminoglycoside antibiotic tolerance
Authors: Wang, Y.J. / Wu, Z.W. / Ji, Q.J.
History
DepositionJul 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MurR/RpiR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9812
Polymers31,7221
Non-polymers2581
Water2,810156
1
A: MurR/RpiR family transcriptional regulator
hetero molecules

A: MurR/RpiR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9614
Polymers63,4452
Non-polymers5162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6770 Å2
ΔGint-44 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.138, 81.624, 137.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

21A-498-

HOH

31A-552-

HOH

41A-556-

HOH

-
Components

#1: Protein MurR/RpiR family transcriptional regulator / Transcriptional regulatory protein RccR


Mass: 31722.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ybbH / Production host: Escherichia coli (E. coli) / References: UniProt: A0A071KWR3
#2: Chemical ChemComp-ELE / 2-keto 3 deoxy 6 phospho gluconate


Mass: 258.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M DL-malic acid pH 7.0, 0.1 M imidazole pH 7.0, 22% polyethylene glycol monomethyl ether 550 (v/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26374 / % possible obs: 75.21 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 25.4
Reflection shellResolution: 1.901→1.969 Å / Rmerge(I) obs: 0.652 / Num. unique obs: 26374

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→26.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.571 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24252 1357 5.1 %RANDOM
Rwork0.199 ---
obs0.20127 25023 75.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 16 156 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122174
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162106
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.6492945
X-RAY DIFFRACTIONr_angle_other_deg0.491.5814842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.685280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.764515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11410373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
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_it3.0953.0171123
X-RAY DIFFRACTIONr_mcbond_other3.0933.0161123
X-RAY DIFFRACTIONr_mcangle_it4.5615.4161402
X-RAY DIFFRACTIONr_mcangle_other4.565.4191403
X-RAY DIFFRACTIONr_scbond_it4.073.4281051
X-RAY DIFFRACTIONr_scbond_other4.0783.4391044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2116.081544
X-RAY DIFFRACTIONr_long_range_B_refined8.32432.142530
X-RAY DIFFRACTIONr_long_range_B_other8.32432.132531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 44 -
Rwork0.269 851 -
obs--35.32 %

+
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