[English] 日本語
Yorodumi
- PDB-4etz: Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4etz
TitleCrystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1
ComponentsPelD
KeywordsSIGNALING PROTEIN / c-di-GMP
Function / homology
Function and homology information


cyclic-di-GMP binding / polysaccharide biosynthetic process / single-species biofilm formation / membrane
Similarity search - Function
Alpha-Beta Plaits - #2880 / PelD, GGDEF domain / PelD, GGDEF domain superfamily / PelD GGDEF domain / GAF domain / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...Alpha-Beta Plaits - #2880 / PelD, GGDEF domain / PelD, GGDEF domain superfamily / PelD GGDEF domain / GAF domain / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLi, Z. / Chen, J. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structures of the PelD Cyclic Diguanylate Effector Involved in Pellicle Formation in Pseudomonas aeruginosa PAO1.
Authors: Li, Z. / Chen, J.H. / Hao, Y. / Nair, S.K.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PelD
B: PelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2334
Polymers66,8522
Non-polymers1,3812
Water2,522140
1
A: PelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1172
Polymers33,4261
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PelD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1172
Polymers33,4261
Non-polymers6901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.320, 41.310, 110.850
Angle α, β, γ (deg.)90.000, 95.450, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PelD


Mass: 33426.098 Da / Num. of mol.: 2 / Fragment: UNP residues 158-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3061, pelD / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3) / References: UniProt: Q9HZE7
#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


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 200 mM Li2SO4, and 1.26 M (NH4)2SO4, hanging drop, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.05 Å / Num. obs: 40304 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.001 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.150.8972.3128833531599.8
2.15-2.250.5843.74262604414100
2.25-2.350.4165.0921944369299.8
2.35-2.450.3036.7418700314199.9
2.45-2.550.2388.25157182652100
2.55-2.80.15211.9130354511899.8
2.8-30.09616.8917378293299.8
3-4.30.04529.9149470854699.7
4.3-5.30.03539.3411613206499.6
5.3-70.03638.287565136799.3
7-500.03139.125320106397.2
50

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.433 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 2015 5 %RANDOM
Rwork0.2305 ---
obs0.2328 40287 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.53 Å2 / Biso mean: 53.403 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å20.11 Å2
2---0.74 Å20 Å2
3---3.19 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 92 140 4768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224698
X-RAY DIFFRACTIONr_angle_refined_deg1.512.0276374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67323.025238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29415812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4931562
X-RAY DIFFRACTIONr_chiral_restr0.1010.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213558
X-RAY DIFFRACTIONr_mcbond_it0.7761.52846
X-RAY DIFFRACTIONr_mcangle_it1.44424526
X-RAY DIFFRACTIONr_scbond_it1.99131852
X-RAY DIFFRACTIONr_scangle_it3.254.51848
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 146 -
Rwork0.294 2768 -
all-2914 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.85420.91811.88910.96820.30180.9988-0.0328-0.44470.16490.0803-0.02020.174-0.05380.02630.0530.14870.01130.02480.1153-0.00970.074422.0717-0.140711.816
27.1765-0.6552-2.40051.14280.25540.94120.03890.39080.0036-0.1061-0.05010.28560.01390.03210.01120.27610.0001-0.03160.27490.00260.115317.3539-18.767143.3493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A158 - 454
2X-RAY DIFFRACTION2B158 - 454

+
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