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

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Basic information

Entry
Database: PDB / ID: 8evy
TitleDdlB from Pseudomonas aeruginosa PAO1 in complex with ATP and D-ala-D-ala
ComponentsD-alanine--D-alanine ligase B
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 B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
B: D-alanine--D-alanine ligase B
A: D-alanine--D-alanine ligase B
C: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,68419
Polymers103,4593
Non-polymers2,22516
Water4,179232
1
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)70,44112
Polymers68,9732
Non-polymers1,46810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area3730 Å2
ΔGint-66 kcal/mol
Surface area24250 Å2
MethodPISA
2
A: D-alanine--D-alanine ligase B
C: D-alanine--D-alanine ligase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46413
Polymers68,9732
Non-polymers1,49111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-75 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.587, 198.892, 177.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules BAC

#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

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Non-polymers , 5 types, 248 molecules

#2: Chemical
ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.81 Å3/Da / Density % sol: 67.74 %
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: 2.35→39.8 Å / Num. obs: 66359 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.043 / Rrim(I) all: 0.161 / Χ2: 0.96 / Net I/σ(I): 13.7 / Num. measured all: 920367
Reflection shellResolution: 2.35→2.41 Å / % possible obs: 99.9 % / Redundancy: 14.4 % / Rmerge(I) obs: 1.944 / Num. measured all: 63556 / Num. unique obs: 4413 / CC1/2: 0.699 / Rpim(I) all: 0.529 / Rrim(I) all: 2.016 / Χ2: 0.86 / Net I/σ(I) obs: 1.5

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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: 2.35→39.8 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 3382 5.1 %
Rwork0.2104 --
obs0.2123 66305 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7132 0 100 232 7464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027351
X-RAY DIFFRACTIONf_angle_d0.5299982
X-RAY DIFFRACTIONf_dihedral_angle_d25.2152635
X-RAY DIFFRACTIONf_chiral_restr0.041129
X-RAY DIFFRACTIONf_plane_restr0.0051289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.38371110.33062624X-RAY DIFFRACTION100
2.38-2.420.34361420.30922604X-RAY DIFFRACTION100
2.42-2.460.34011480.28912554X-RAY DIFFRACTION100
2.46-2.50.38091210.29622627X-RAY DIFFRACTION100
2.5-2.540.38171220.27852614X-RAY DIFFRACTION100
2.54-2.590.32821390.26442579X-RAY DIFFRACTION100
2.59-2.640.3341610.26982588X-RAY DIFFRACTION100
2.64-2.690.30921410.26112594X-RAY DIFFRACTION100
2.69-2.750.33411460.24272593X-RAY DIFFRACTION100
2.75-2.810.29151330.23632620X-RAY DIFFRACTION100
2.81-2.880.29191530.23762590X-RAY DIFFRACTION100
2.88-2.960.33431310.25332606X-RAY DIFFRACTION100
2.96-3.050.29621460.25942601X-RAY DIFFRACTION100
3.05-3.150.24911490.2362583X-RAY DIFFRACTION100
3.15-3.260.25381540.21562620X-RAY DIFFRACTION100
3.26-3.390.26211380.22082626X-RAY DIFFRACTION100
3.39-3.540.27131400.20132612X-RAY DIFFRACTION100
3.54-3.730.23351380.20392641X-RAY DIFFRACTION100
3.73-3.960.22141570.19552605X-RAY DIFFRACTION100
3.96-4.270.2251330.17732655X-RAY DIFFRACTION100
4.27-4.70.19941480.16812641X-RAY DIFFRACTION100
4.7-5.380.19411470.1772656X-RAY DIFFRACTION100
5.38-6.770.24461380.21122696X-RAY DIFFRACTION100
6.77-39.80.18781460.16952794X-RAY DIFFRACTION100

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