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- PDB-7u9k: Staphylococcus aureus D-alanine-D-alanine ligase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7u9k
TitleStaphylococcus aureus D-alanine-D-alanine ligase in complex with ATP, D-ala-D-ala, Mg2+ and K+
Components
  • D-alanine--D-alanine ligase
  • DAL-DAL
KeywordsLIGASE / ATP-grasp / nucleotide binding / metal binding
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 / Rossmann fold - #20 / ATP-grasp fold, A domain ...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 / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / : / polypeptide(D) / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsPederick, J.L. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem. / Year: 2023
Title: Structure-guided design and synthesis of ATP-competitive N-acyl-substituted sulfamide d-alanine-d-alanine ligase inhibitors.
Authors: Becker, R. / Pederick, J.L. / Dawes, E.G. / Bruning, J.B. / Abell, A.D.
History
DepositionMar 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanine--D-alanine ligase
B: D-alanine--D-alanine ligase
F: DAL-DAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,99711
Polymers82,8573
Non-polymers1,1398
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-40 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.447, 70.058, 91.598
Angle α, β, γ (deg.)90.000, 102.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Polypeptide(D) , 2 types, 3 molecules ABF

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


Mass: 41348.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: ddl, SAOUHSC_02318 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FWH3, D-alanine-D-alanine ligase
#2: Polypeptide(D) DAL-DAL


Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: D-alanine-D-alanine dipeptide product formed by D-alanine-D-alanine ligase
Source: (synth.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

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Non-polymers , 5 types, 290 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 20 - 30% PEG 3350, 0.5 M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→38.02 Å / Num. obs: 43862 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.093 / Rrim(I) all: 0.236 / Net I/σ(I): 9.3 / Num. measured all: 289114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.057.20.6932308532170.7670.280.7482.9100
8.94-38.026.30.07232595180.9940.030.07822.698.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I87

2i87


Resolution: 2→37.68 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 2160 4.93 %
Rwork0.2395 41680 -
obs0.2413 43840 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.29 Å2 / Biso mean: 32.1961 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: final / Resolution: 2→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5141 0 75 282 5498
Biso mean--28.02 33.83 -
Num. residues----662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.36741420.308127662908100
2.05-2.10.30261470.284227772924100
2.1-2.150.34811330.263527232856100
2.15-2.220.32611230.275928252948100
2.22-2.290.30741490.271327772926100
2.29-2.370.32251350.265227642899100
2.37-2.470.30321350.267527672902100
2.47-2.580.3211570.267127802937100
2.58-2.710.31121590.275727102869100
2.71-2.880.31471420.261828172959100
2.88-3.110.32511110.260527922903100
3.11-3.420.25791450.250127912936100
3.42-3.910.27421680.222727672935100
3.91-4.930.23031430.18952784292799
4.93-37.680.21881710.201228403011100

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