[English] 日本語
Yorodumi
- PDB-7vhv: Crystal structure of S. aureus D-alanine alanyl carrier protein ligase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vhv
TitleCrystal structure of S. aureus D-alanine alanyl carrier protein ligase
ComponentsD-alanine--D-alanyl carrier protein ligase
KeywordsLIGASE / D-alanine / Dlt operon
Function / homology
Function and homology information


D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
D-alanine--D-alanyl carrier protein ligase / D-alanine:D-alanyl carrier protein ligase-like / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / D-alanine--D-alanyl carrier protein ligase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLee, B.J. / Lee, I.-G. / Im, H.G. / Yoon, H.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1F1A1050961 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A5A2024425 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural and functional analysis of the D-alanyl carrier protein ligase DltA from Staphylococcus aureus Mu50.
Authors: Lee, I.G. / Song, C. / Yang, S. / Jeon, H. / Park, J. / Yoon, H.J. / Im, H. / Kang, S.M. / Eun, H.J. / Lee, B.J.
History
DepositionSep 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)220,90712
Polymers218,7814
Non-polymers2,1268
Water6,864381
1
C: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2273
Polymers54,6951
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-12 kcal/mol
Surface area20180 Å2
MethodPISA
2
D: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2273
Polymers54,6951
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-12 kcal/mol
Surface area20720 Å2
MethodPISA
3
B: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2273
Polymers54,6951
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-12 kcal/mol
Surface area20080 Å2
MethodPISA
4
A: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2273
Polymers54,6951
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-12 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.468, 88.510, 130.850
Angle α, β, γ (deg.)90.000, 91.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2 or (resid 3 and (name...
21(chain B and (resseq 2 or (resid 3 and (name...
31(chain C and (resseq 2 or (resid 3 and (name...
41(chain D and (resseq 2 or (resid 3 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 2 or (resid 3 and (name...A2
121(chain A and (resseq 2 or (resid 3 and (name...A3
131(chain A and (resseq 2 or (resid 3 and (name...A1 - 511
141(chain A and (resseq 2 or (resid 3 and (name...A1 - 511
151(chain A and (resseq 2 or (resid 3 and (name...A1 - 511
161(chain A and (resseq 2 or (resid 3 and (name...A1 - 511
171(chain A and (resseq 2 or (resid 3 and (name...A1 - 511
181(chain A and (resseq 2 or (resid 3 and (name...A1 - 511
211(chain B and (resseq 2 or (resid 3 and (name...B2
221(chain B and (resseq 2 or (resid 3 and (name...B3
231(chain B and (resseq 2 or (resid 3 and (name...B1 - 511
241(chain B and (resseq 2 or (resid 3 and (name...B1 - 511
251(chain B and (resseq 2 or (resid 3 and (name...B1 - 511
261(chain B and (resseq 2 or (resid 3 and (name...B1 - 511
271(chain B and (resseq 2 or (resid 3 and (name...B1 - 511
281(chain B and (resseq 2 or (resid 3 and (name...B1 - 511
311(chain C and (resseq 2 or (resid 3 and (name...C2
321(chain C and (resseq 2 or (resid 3 and (name...C3
331(chain C and (resseq 2 or (resid 3 and (name...C2 - 511
341(chain C and (resseq 2 or (resid 3 and (name...C2 - 511
351(chain C and (resseq 2 or (resid 3 and (name...C2 - 511
361(chain C and (resseq 2 or (resid 3 and (name...C2 - 511
371(chain C and (resseq 2 or (resid 3 and (name...C2 - 511
411(chain D and (resseq 2 or (resid 3 and (name...D2
421(chain D and (resseq 2 or (resid 3 and (name...D3
431(chain D and (resseq 2 or (resid 3 and (name...D2 - 511
441(chain D and (resseq 2 or (resid 3 and (name...D2 - 511
451(chain D and (resseq 2 or (resid 3 and (name...D2 - 511
461(chain D and (resseq 2 or (resid 3 and (name...D2 - 511
471(chain D and (resseq 2 or (resid 3 and (name...D2 - 511
481(chain D and (resseq 2 or (resid 3 and (name...D2 - 511

-
Components

#1: Protein
D-alanine--D-alanyl carrier protein ligase / DCL / D-alanine--poly(phosphoribitol) ligase subunit 1 / D-alanine-activating enzyme / DAE


Mass: 54695.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: dltA, SAV0932 / Production host: Escherichia coli (E. coli)
References: UniProt: P68876, D-alanine-[D-alanyl-carrier protein] ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 5% PEG 4K, 0.16 M Magnesium acetate, 0.1 M Na. cacodylate, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. obs: 66485 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.9613 / Net I/σ(I): 10.3
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 8768 / CC1/2: 0.8217

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FCC

3fcc


Resolution: 2.55→39.911 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1994 3 %
Rwork0.1893 64491 -
obs0.1909 66485 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.85 Å2 / Biso mean: 48.0957 Å2 / Biso min: 21.31 Å2
Refinement stepCycle: final / Resolution: 2.55→39.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15286 0 128 381 15795
Biso mean--42.23 42.97 -
Num. residues----1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215722
X-RAY DIFFRACTIONf_angle_d1.48921336
X-RAY DIFFRACTIONf_chiral_restr0.0862422
X-RAY DIFFRACTIONf_plane_restr0.0092732
X-RAY DIFFRACTIONf_dihedral_angle_d16.6089528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7957X-RAY DIFFRACTION11.676TORSIONAL
12B7957X-RAY DIFFRACTION11.676TORSIONAL
13C7957X-RAY DIFFRACTION11.676TORSIONAL
14D7957X-RAY DIFFRACTION11.676TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.55-2.61380.33691380.2636449598
2.6138-2.68450.31151380.24484625100
2.6845-2.76340.31121420.24074564100
2.7634-2.85260.29751360.25734641100
2.8526-2.95450.37181490.2424576100
2.9545-3.07280.2961380.23284603100
3.0728-3.21260.27631500.22074600100
3.2126-3.38190.2871480.20974581100
3.3819-3.59360.23861400.191462099
3.5936-3.87090.23521420.18284585100
3.8709-4.260.20931490.167458899
4.26-4.87550.20521410.1511461399
4.8755-6.1390.19271380.1694654100
6.139-39.9110.17691450.1523474699

+
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://pdbjlvh1.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