[English] 日本語
Yorodumi
- PDB-4rnj: PaMorA phosphodiesterase domain, apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rnj
TitlePaMorA phosphodiesterase domain, apo form
ComponentsMotility regulator
KeywordsHYDROLASE / EAL domain / Phosphodiesterase / c-di-GMP
Function / homology
Function and homology information


c-di-GMP signaling / cyclic-guanylate-specific phosphodiesterase / diguanylate cyclase activity / nucleotide binding / regulation of DNA-templated transcription / metal ion binding / identical protein binding / membrane
Similarity search - Function
: / EAL domain / Putative diguanylate phosphodiesterase / PAS fold-3 / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / PAS fold / Diguanylate cyclase, GGDEF domain ...: / EAL domain / Putative diguanylate phosphodiesterase / PAS fold-3 / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
cyclic-guanylate-specific phosphodiesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPhippen, C.W. / Tews, I.
CitationJournal: Febs Lett. / Year: 2014
Title: Formation and dimerization of the phosphodiesterase active site of the Pseudomonas aeruginosa MorA, a bi-functional c-di-GMP regulator.
Authors: Phippen, C.W. / Mikolajek, H. / Schlaefli, H.G. / Keevil, C.W. / Webb, J.S. / Tews, I.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Motility regulator
B: Motility regulator


Theoretical massNumber of molelcules
Total (without water)63,4552
Polymers63,4552
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Motility regulator


Theoretical massNumber of molelcules
Total (without water)31,7271
Polymers31,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Motility regulator


Theoretical massNumber of molelcules
Total (without water)31,7271
Polymers31,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.071, 79.895, 138.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsActive diguanylate cyclase

-
Components

#1: Protein Motility regulator


Mass: 31727.320 Da / Num. of mol.: 2 / Fragment: EAL domain, UNP residues 1145-1409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01 / Gene: morA, PA4601 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9HVI8, cyclic-guanylate-specific phosphodiesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Imidazole; MES, 0.09M NaN03; Na2HPO4; (NH4)2SO4, 30% Ethylene glycol; PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 14, 2012
RadiationMonochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.32→100 Å / Num. all: 25794 / Num. obs: 25720 / % possible obs: 99.7 % / Redundancy: 4.28 % / Biso Wilson estimate: 42.67 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.87
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4

-
Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N3T

3n3t


Resolution: 2.32→48.741 Å / FOM work R set: 0.8062 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1310 5.09 %RANDOM
Rwork0.1968 ---
obs0.1997 25717 99.71 %-
all-25794 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.79 Å2 / Biso mean: 47.68 Å2 / Biso min: 25.23 Å2
Refinement stepCycle: LAST / Resolution: 2.32→48.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 0 117 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134056
X-RAY DIFFRACTIONf_angle_d1.4315488
X-RAY DIFFRACTIONf_chiral_restr0.084612
X-RAY DIFFRACTIONf_plane_restr0.007720
X-RAY DIFFRACTIONf_dihedral_angle_d15.1461519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.41290.33351300.28462650278099
2.4129-2.52270.31961430.263626762819100
2.5227-2.65570.29711650.238526672832100
2.6557-2.82210.27931300.232626802810100
2.8221-3.03990.30551580.228626662824100
3.0399-3.34580.28921280.222527242852100
3.3458-3.82980.26271600.198627092869100
3.8298-4.82440.1951550.157627442899100
4.8244-48.75160.22141410.165928913032100

+
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