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- PDB-8evz: DdlB from Pseudomonas aeruginosa PAO1 in complex with ADP and pho... -

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Basic information

Entry
Database: PDB / ID: 8evz
TitleDdlB from Pseudomonas aeruginosa PAO1 in complex with ADP and phosphorylated D-cycloserine
ComponentsD-alanine--D-alanine ligase B
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 B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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
B: D-alanine--D-alanine ligase B
C: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,43315
Polymers103,4593
Non-polymers1,97412
Water5,441302
1
A: D-alanine--D-alanine ligase B
C: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,28810
Polymers68,9732
Non-polymers1,3168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-78 kcal/mol
Surface area23770 Å2
MethodPISA
2
B: D-alanine--D-alanine ligase B
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)70,28810
Polymers68,9732
Non-polymers1,3168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3650 Å2
ΔGint-77 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.664, 199.046, 177.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 34486.297 Da / Num. of mol.: 3
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: ddlB, PA4410 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LCT6, D-alanine-D-alanine ligase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 182.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7N2O5P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH 7.8, 5% gamma-PGA (Na+ form, LM), 30% PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.45→39.66 Å / Num. obs: 59127 / % possible obs: 99.9 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.056 / Rrim(I) all: 0.209 / Χ2: 0.98 / Net I/σ(I): 12.8 / Num. measured all: 816987
Reflection shellResolution: 2.45→2.52 Å / % possible obs: 99.9 % / Redundancy: 14.3 % / Rmerge(I) obs: 2.055 / Num. measured all: 65381 / Num. unique obs: 4569 / CC1/2: 0.65 / Rpim(I) all: 0.559 / Rrim(I) all: 2.13 / Χ2: 0.88 / Net I/σ(I) obs: 1.5

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Processing

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

8evy


Resolution: 2.45→39.66 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 3044 5.15 %
Rwork0.2036 --
obs0.2057 59077 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7062 0 120 302 7484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037305
X-RAY DIFFRACTIONf_angle_d0.6749924
X-RAY DIFFRACTIONf_dihedral_angle_d11.4461059
X-RAY DIFFRACTIONf_chiral_restr0.0431119
X-RAY DIFFRACTIONf_plane_restr0.0051281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.34271290.29812532X-RAY DIFFRACTION100
2.49-2.530.39391290.29572498X-RAY DIFFRACTION100
2.53-2.570.35971220.27522531X-RAY DIFFRACTION100
2.57-2.620.35251520.27642508X-RAY DIFFRACTION100
2.62-2.670.3271440.27232546X-RAY DIFFRACTION100
2.67-2.720.31341380.25282507X-RAY DIFFRACTION100
2.72-2.780.30961280.23812515X-RAY DIFFRACTION100
2.78-2.850.31571520.23682533X-RAY DIFFRACTION100
2.85-2.920.28591310.24582511X-RAY DIFFRACTION100
2.92-30.31161280.26232534X-RAY DIFFRACTION100
3-3.090.30191460.25322521X-RAY DIFFRACTION100
3.09-3.190.28061560.23442518X-RAY DIFFRACTION100
3.19-3.30.26571430.2262566X-RAY DIFFRACTION100
3.3-3.430.2771300.21442539X-RAY DIFFRACTION100
3.43-3.590.29211280.20242545X-RAY DIFFRACTION100
3.59-3.780.25581500.20242554X-RAY DIFFRACTION100
3.78-4.010.21841470.18632535X-RAY DIFFRACTION100
4.01-4.320.19751320.15852583X-RAY DIFFRACTION100
4.32-4.760.1831400.15562568X-RAY DIFFRACTION100
4.76-5.440.1781430.15772567X-RAY DIFFRACTION100
5.44-6.850.20951330.20032617X-RAY DIFFRACTION99
6.85-39.660.18681430.16842705X-RAY DIFFRACTION100

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