[English] 日本語
Yorodumi
- PDB-8evz: DdlB from Pseudomonas aeruginosa PAO1 in complex with ADP and pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8evz
TitleDdlB from Pseudomonas aeruginosa PAO1 in complex with ADP and phosphorylated D-cycloserine
ComponentsD-alanine--D-alanine ligase B
KeywordsLIGASE/INHIBITOR / ATP-grasp / LIGASE / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-DS0 / D-alanine--D-alanine ligase B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPederick, J.L. / Woolman, J.C. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: Comparative functional and structural analysis of Pseudomonas aeruginosa d-alanine-d-alanine ligase isoforms as prospective antibiotic targets.
Authors: Pederick, J.L. / Woolman, J.C. / Bruning, J.B.
History
DepositionOct 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-alanine--D-alanine ligase B
B: D-alanine--D-alanine ligase B
C: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,43315
Polymers103,4593
Non-polymers1,97412
Water5,441302
1
A: D-alanine--D-alanine ligase B
C: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,28810
Polymers68,9732
Non-polymers1,3168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-78 kcal/mol
Surface area23770 Å2
MethodPISA
2
B: D-alanine--D-alanine ligase B
hetero molecules

B: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,28810
Polymers68,9732
Non-polymers1,3168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3650 Å2
ΔGint-77 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.664, 199.046, 177.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein D-alanine--D-alanine ligase B / D-Ala-D-Ala ligase B / D-alanylalanine synthetase B


Mass: 34486.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ddlB, PA4410 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LCT6, D-alanine-D-alanine ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-DS0 / [(4R)-4-azanyl-4,5-dihydro-1,2-oxazol-3-yl] dihydrogen phosphate


Mass: 182.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7N2O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH 7.8, 5% gamma-PGA (Na+ form, LM), 30% PEG 500 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.45→39.66 Å / Num. obs: 59127 / % possible obs: 99.9 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.056 / Rrim(I) all: 0.209 / Χ2: 0.98 / Net I/σ(I): 12.8 / Num. measured all: 816987
Reflection shellResolution: 2.45→2.52 Å / % possible obs: 99.9 % / Redundancy: 14.3 % / Rmerge(I) obs: 2.055 / Num. measured all: 65381 / Num. unique obs: 4569 / CC1/2: 0.65 / Rpim(I) all: 0.559 / Rrim(I) all: 2.13 / Χ2: 0.88 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8EVY

8evy


Resolution: 2.45→39.66 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 3044 5.15 %
Rwork0.2036 --
obs0.2057 59077 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7062 0 120 302 7484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037305
X-RAY DIFFRACTIONf_angle_d0.6749924
X-RAY DIFFRACTIONf_dihedral_angle_d11.4461059
X-RAY DIFFRACTIONf_chiral_restr0.0431119
X-RAY DIFFRACTIONf_plane_restr0.0051281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.34271290.29812532X-RAY DIFFRACTION100
2.49-2.530.39391290.29572498X-RAY DIFFRACTION100
2.53-2.570.35971220.27522531X-RAY DIFFRACTION100
2.57-2.620.35251520.27642508X-RAY DIFFRACTION100
2.62-2.670.3271440.27232546X-RAY DIFFRACTION100
2.67-2.720.31341380.25282507X-RAY DIFFRACTION100
2.72-2.780.30961280.23812515X-RAY DIFFRACTION100
2.78-2.850.31571520.23682533X-RAY DIFFRACTION100
2.85-2.920.28591310.24582511X-RAY DIFFRACTION100
2.92-30.31161280.26232534X-RAY DIFFRACTION100
3-3.090.30191460.25322521X-RAY DIFFRACTION100
3.09-3.190.28061560.23442518X-RAY DIFFRACTION100
3.19-3.30.26571430.2262566X-RAY DIFFRACTION100
3.3-3.430.2771300.21442539X-RAY DIFFRACTION100
3.43-3.590.29211280.20242545X-RAY DIFFRACTION100
3.59-3.780.25581500.20242554X-RAY DIFFRACTION100
3.78-4.010.21841470.18632535X-RAY DIFFRACTION100
4.01-4.320.19751320.15852583X-RAY DIFFRACTION100
4.32-4.760.1831400.15562568X-RAY DIFFRACTION100
4.76-5.440.1781430.15772567X-RAY DIFFRACTION100
5.44-6.850.20951330.20032617X-RAY DIFFRACTION99
6.85-39.660.18681430.16842705X-RAY DIFFRACTION100

+
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