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- PDB-8evx: DdlA from Pseudomonas aeruginosa PAO1 in complex with ADP and pho... -

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Basic information

Entry
Database: PDB / ID: 8evx
TitleDdlA from Pseudomonas aeruginosa PAO1 in complex with ADP and phosphorylated D-cycloserine
ComponentsD-alanine--D-alanine ligase A
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 A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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)74,71512
Polymers73,3212
Non-polymers1,39410
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-68 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.467, 133.053, 53.852
Angle α, β, γ (deg.)90.00, 109.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 36660.680 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

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Non-polymers , 5 types, 652 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 182.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N2O5P / 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium Sodium Tartrate tetrahydrate, 20% 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: 1.55→39.15 Å / Num. obs: 84998 / % possible obs: 93.5 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.041 / Rrim(I) all: 0.109 / Χ2: 0.75 / Net I/σ(I): 10.9 / Num. measured all: 558968
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 92.4 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.449 / Num. measured all: 24330 / Num. unique obs: 4160 / CC1/2: 0.899 / Rpim(I) all: 0.195 / Rrim(I) all: 0.492 / Χ2: 0.35 / Net I/σ(I) obs: 2.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

8evw


Resolution: 1.55→37.18 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 4372 5.15 %
Rwork0.1984 --
obs0.1994 84946 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4575 0 82 642 5299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034748
X-RAY DIFFRACTIONf_angle_d0.8296454
X-RAY DIFFRACTIONf_dihedral_angle_d12.872697
X-RAY DIFFRACTIONf_chiral_restr0.049748
X-RAY DIFFRACTIONf_plane_restr0.006837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.31341370.25312628X-RAY DIFFRACTION92
1.57-1.590.27011580.23832689X-RAY DIFFRACTION92
1.59-1.610.2591190.22662603X-RAY DIFFRACTION92
1.61-1.630.25931550.22652661X-RAY DIFFRACTION92
1.63-1.650.26331350.22912649X-RAY DIFFRACTION92
1.65-1.670.23871480.21212616X-RAY DIFFRACTION93
1.67-1.690.25011530.21592647X-RAY DIFFRACTION91
1.69-1.720.23631440.2112624X-RAY DIFFRACTION92
1.72-1.750.24861440.20642654X-RAY DIFFRACTION91
1.75-1.770.25191410.21132587X-RAY DIFFRACTION92
1.77-1.80.25481390.20892648X-RAY DIFFRACTION92
1.8-1.840.23051390.21892645X-RAY DIFFRACTION91
1.84-1.870.25071170.22062571X-RAY DIFFRACTION90
1.87-1.910.24161270.21222374X-RAY DIFFRACTION81
1.91-1.950.25811540.21252508X-RAY DIFFRACTION88
1.95-20.27141700.21092694X-RAY DIFFRACTION94
2-2.050.22351200.20062827X-RAY DIFFRACTION96
2.05-2.10.23821540.20242706X-RAY DIFFRACTION95
2.1-2.170.20921430.19962777X-RAY DIFFRACTION95
2.17-2.240.22881630.19792736X-RAY DIFFRACTION96
2.24-2.320.22551380.19722773X-RAY DIFFRACTION96
2.32-2.410.22341560.19482777X-RAY DIFFRACTION96
2.41-2.520.20891560.1982834X-RAY DIFFRACTION98
2.52-2.650.2331340.20012801X-RAY DIFFRACTION97
2.65-2.820.23171580.20832821X-RAY DIFFRACTION97
2.82-3.030.21031600.2042732X-RAY DIFFRACTION96
3.03-3.340.2051510.1972725X-RAY DIFFRACTION94
3.34-3.820.19091340.18242475X-RAY DIFFRACTION86
3.82-4.810.16861510.16632891X-RAY DIFFRACTION99
4.81-37.180.18591740.192901X-RAY DIFFRACTION99

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