[English] 日本語
Yorodumi
- PDB-5xge: Crystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xge
TitleCrystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseudomonas aeruginosa in complex with cyclic di-GMP
ComponentsUncharacterized protein PA0861
KeywordsTRANSCRIPTION / PAS domain / GGDEF-EAL domain / Pseudomonas aeruginosa / Biofilm / RbdA / PA0861 / cyclic di-GMP
Function / homology
Function and homology information


regulation of DNA-templated transcription / membrane
Similarity search - Function
Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase ...Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Chem-C2E / EAL domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.31 Å
AuthorsLiu, C. / Liew, C.W. / Sreekanth, R. / Lescar, J.
CitationJournal: J. Bacteriol. / Year: 2018
Title: Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa.
Authors: Liu, C. / Liew, C.W. / Wong, Y.H. / Tan, S.T. / Poh, W.H. / Manimekalai, M.S.S. / Rajan, S. / Xin, L. / Liang, Z.X. / Gruber, G. / Rice, S.A. / Lescar, J.
History
DepositionApr 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein PA0861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1762
Polymers63,4851
Non-polymers6901
Water2,540141
1
A: Uncharacterized protein PA0861
hetero molecules

A: Uncharacterized protein PA0861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3514
Polymers126,9712
Non-polymers1,3812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area9410 Å2
ΔGint-52 kcal/mol
Surface area46920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.881, 134.881, 211.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Uncharacterized protein PA0861


Mass: 63485.305 Da / Num. of mol.: 1 / Fragment: UNP residues 233-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0861 / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9I580
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES/imidazole at pH 6.5, 0.1M carboxylic acid, 10% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.31→48.7 Å / Num. obs: 11308 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 93.44 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 11.3
Reflection shellResolution: 3.31→3.49 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.618 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 3.31→48.12 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.852 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.528
RfactorNum. reflection% reflectionSelection details
Rfree0.255 565 5.01 %RANDOM
Rwork0.18 ---
obs0.184 11285 100 %-
Displacement parametersBiso mean: 58.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.8399 Å20 Å20 Å2
2---0.8399 Å20 Å2
3---1.6799 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 3.31→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 46 141 4482
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094424HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.126001HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1556SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes644HARMONIC5
X-RAY DIFFRACTIONt_it4424HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion22.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5175SEMIHARMONIC4
LS refinement shellResolution: 3.31→3.63 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2468 133 4.99 %
Rwork0.1753 2530 -
all0.1789 2663 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 40.0572 Å / Origin y: 0.9174 Å / Origin z: 91.3356 Å
111213212223313233
T-0.1673 Å20.0236 Å20.0752 Å2--0.1296 Å2-0.0691 Å2---0.0996 Å2
L0.9129 °20.1135 °20.2635 °2-0.4578 °20.0153 °2--1.3899 °2
S0.02 Å °0.0591 Å °0.0228 Å °-0.069 Å °0.041 Å °-0.0903 Å °-0.1044 Å °0.1876 Å °-0.061 Å °
Refinement TLS groupSelection details: { A|* }

+
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