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- PDB-8evv: Apo form of DdlA from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 8evv
TitleApo form of DdlA from Pseudomonas aeruginosa PAO1
ComponentsD-alanine--D-alanine ligase A
KeywordsLIGASE / ATP-grasp
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
D-alanine--D-alanine ligase A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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
C: D-alanine--D-alanine ligase A
D: D-alanine--D-alanine ligase A


Theoretical massNumber of molelcules
Total (without water)146,5234
Polymers146,5234
Non-polymers00
Water16,502916
1
A: D-alanine--D-alanine ligase A
C: D-alanine--D-alanine ligase A


Theoretical massNumber of molelcules
Total (without water)73,2612
Polymers73,2612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area26720 Å2
MethodPISA
2
B: D-alanine--D-alanine ligase A
D: D-alanine--D-alanine ligase A


Theoretical massNumber of molelcules
Total (without water)73,2612
Polymers73,2612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-7 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.372, 80.329, 271.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Calcium acetate hydrate, 20% PEG 3350

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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: 2.05→39.73 Å / Num. obs: 99163 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.046 / Rrim(I) all: 0.167 / Χ2: 0.85 / Net I/σ(I): 10.9 / Num. measured all: 1309959
Reflection shellResolution: 2.05→2.09 Å / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 1.306 / Num. measured all: 61181 / Num. unique obs: 4821 / CC1/2: 0.695 / Rpim(I) all: 0.38 / Rrim(I) all: 1.361 / Χ2: 0.51 / 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: 6U1C

6u1c


Resolution: 2.05→39.73 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2516 4951 5.09 %
Rwork0.2115 --
obs0.2136 97252 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9243 0 0 916 10159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029380
X-RAY DIFFRACTIONf_angle_d0.52212696
X-RAY DIFFRACTIONf_dihedral_angle_d14.685626
X-RAY DIFFRACTIONf_chiral_restr0.041492
X-RAY DIFFRACTIONf_plane_restr0.0051669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.28551440.25473132X-RAY DIFFRACTION100
2.07-2.10.30511770.24713100X-RAY DIFFRACTION100
2.1-2.120.2871570.24463061X-RAY DIFFRACTION100
2.12-2.150.29611710.24163135X-RAY DIFFRACTION100
2.15-2.180.26411670.24893080X-RAY DIFFRACTION100
2.18-2.210.25631790.25323058X-RAY DIFFRACTION100
2.21-2.240.43511060.40622261X-RAY DIFFRACTION72
2.24-2.270.5451390.48942237X-RAY DIFFRACTION73
2.27-2.310.26291540.23043138X-RAY DIFFRACTION100
2.31-2.350.26191620.22063089X-RAY DIFFRACTION100
2.35-2.390.24781610.21233138X-RAY DIFFRACTION100
2.39-2.430.28011530.21423089X-RAY DIFFRACTION100
2.43-2.480.27431580.21473135X-RAY DIFFRACTION100
2.48-2.530.26991770.22033084X-RAY DIFFRACTION100
2.53-2.580.26061550.22423131X-RAY DIFFRACTION100
2.58-2.640.28361720.22393105X-RAY DIFFRACTION100
2.64-2.710.31091600.22533106X-RAY DIFFRACTION100
2.71-2.780.30921760.22033115X-RAY DIFFRACTION100
2.78-2.860.25031910.21753120X-RAY DIFFRACTION100
2.86-2.960.24371820.21253114X-RAY DIFFRACTION100
2.96-3.060.24381800.21293094X-RAY DIFFRACTION100
3.06-3.180.24681680.2163141X-RAY DIFFRACTION100
3.18-3.330.27291710.21073143X-RAY DIFFRACTION100
3.33-3.50.21371760.19433142X-RAY DIFFRACTION100
3.5-3.720.24341550.20873149X-RAY DIFFRACTION99
3.72-4.010.2541810.19413154X-RAY DIFFRACTION100
4.01-4.410.18931790.16073153X-RAY DIFFRACTION100
4.41-5.050.20231620.15893233X-RAY DIFFRACTION100
5.05-6.360.23921610.20563257X-RAY DIFFRACTION100
6.36-39.730.22971770.20423407X-RAY DIFFRACTION100

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