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- PDB-8evw: DdlA from Pseudomonas aeruginosa PAO1 in complex with ATP and D-a... -

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Basic information

Entry
Database: PDB / ID: 8evw
TitleDdlA from Pseudomonas aeruginosa PAO1 in complex with ATP and D-ala-D-ala
ComponentsD-alanine--D-alanine ligase A
KeywordsLIGASE/PRODUCT / ATP-grasp / LIGASE / LIGASE-PRODUCT 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, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / 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, C-terminal / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-ala D-ala ligase C-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / D-ALANINE / D-alanine--D-alanine ligase A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 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

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


Theoretical massNumber of molelcules
Total (without water)74,72912
Polymers73,2612
Non-polymers1,46810
Water16,880937
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-53 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.273, 123.615, 53.582
Angle α, β, γ (deg.)90.000, 109.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36630.652 Da / Num. of mol.: 2
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: ddlA, PA4201 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HWI0, D-alanine-D-alanine ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.05M citric acid pH 5.0, 16% PEG3350

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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: Mar 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.22→39.16 Å / Num. obs: 169550 / % possible obs: 98.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 21.8 / Num. measured all: 1148877
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
1.22-1.246.20.3775106182330.9080.1610.4113.897
6.68-39.167.10.03761810720.9990.0120.03356.899.4

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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: 8EVV

8evv


Resolution: 1.22→39.16 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 8680 5.12 %
Rwork0.1604 160814 -
obs0.1614 169494 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.76 Å2 / Biso mean: 17.8965 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 1.22→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 88 937 5738
Biso mean--9.82 28.63 -
Num. residues----647
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.22-1.230.23552940.20955206550097
1.23-1.250.22212860.20225367565397
1.25-1.260.2132950.195250554599
1.26-1.280.20013000.1845363566398
1.28-1.30.21042960.18215302559899
1.3-1.310.20122850.18255328561398
1.31-1.330.21572940.18135359565399
1.33-1.350.20432790.17695380565999
1.35-1.370.21112890.17525337562699
1.37-1.40.21112540.17115437569199
1.4-1.420.21963140.17325323563799
1.42-1.450.19042900.17095393568399
1.45-1.470.17432850.16215395568099
1.47-1.50.16222690.16015368563799
1.5-1.540.19352950.1615359565499
1.54-1.570.17533110.15565313562498
1.57-1.610.17442570.15395207546496
1.61-1.660.16662990.15515367566699
1.66-1.70.19273220.16215383570599
1.7-1.760.18332600.16095429568999
1.76-1.820.17012750.15925425570099
1.82-1.90.18272890.16235410569999
1.9-1.980.1823120.1595374568699
1.98-2.090.18212710.15745372564399
2.09-2.220.1752950.1565401569699
2.22-2.390.18342990.15885414571399
2.39-2.630.18972720.16485449572199
2.63-3.010.18242970.16175137543495
3.01-3.790.16562830.145854735756100
3.79-39.160.16073130.152554935806100

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