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- PDB-7vhv: Crystal structure of S. aureus D-alanine alanyl carrier protein ligase -

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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 / AMP-binding enzyme, C-terminal domain superfamily
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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