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- PDB-8fff: Crystal structure of Staphylococcus aureus D-alanine D-alanine li... -

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Basic information

Entry
Database: PDB / ID: 8fff
TitleCrystal structure of Staphylococcus aureus D-alanine D-alanine ligase enzyme in complex with acetate
ComponentsD-alanine--D-alanine ligase
KeywordsLIGASE / D-alanine D-alanie / S.aureus / cell wall biosynthesis / omega loop
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 / cytoplasm
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
ACETATE ION / D-alanine--D-alanine ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsJayasinghe, Y.P. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI151924 United States
CitationJournal: Biorxiv / Year: 2024
Title: Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity.
Authors: Panda, S. / Jayasinghe, Y.P. / Shinde, D.D. / Bueno, E. / Stastny, A. / Bertrand, B.P. / Chaudhari, S.S. / Kielian, T. / Cava, F. / Ronning, D.R. / Thomas, V.C.
History
DepositionDec 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanine--D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1613
Polymers40,0431
Non-polymers1182
Water2,936163
1
A: D-alanine--D-alanine ligase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)80,3226
Polymers80,0862
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area4750 Å2
ΔGint-12 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.123, 65.817, 99.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 40043.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: ddl, ddl_1, BTN44_12750, CV021_10020, DD547_02119, E4U00_12215, EDCC5055_02053, EP54_12800, EQ90_09645, FA040_09370, G6Y24_11355, GO814_01235, GO942_06460, GQX37_08410, HK402_11205, HUW54_ ...Gene: ddl, ddl_1, BTN44_12750, CV021_10020, DD547_02119, E4U00_12215, EDCC5055_02053, EP54_12800, EQ90_09645, FA040_09370, G6Y24_11355, GO814_01235, GO942_06460, GQX37_08410, HK402_11205, HUW54_10625, NCTC13131_01418, NCTC6133_02837, SAGV69_02521, SAHC1335_00023, SAMEA2077334_02016, SAMEA2078260_01877, SAMEA2078588_01848, SAMEA2080344_01838, SAMEA2081063_01853, SAMEA2081470_01763, SAMEA70146418_02253
Production host: Escherichia coli (E. coli) / References: UniProt: W8TRT0, D-alanine-D-alanine ligase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M NaSCN and 20 % polyethylene glycol monomethyl ether 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.92→49.72 Å / Num. obs: 28387 / % possible obs: 100 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.4
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 1414 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
DIALSdata scaling
DIALSdata reduction
PHENIX1.18.2-3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→49.71 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1601 5.96 %
Rwork0.2097 --
obs0.2126 26871 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 8 163 2908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082803
X-RAY DIFFRACTIONf_angle_d1.0953797
X-RAY DIFFRACTIONf_dihedral_angle_d7.904372
X-RAY DIFFRACTIONf_chiral_restr0.06424
X-RAY DIFFRACTIONf_plane_restr0.006498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.980.4769760.45271108X-RAY DIFFRACTION47
1.98-2.050.38041450.35372287X-RAY DIFFRACTION96
2.05-2.130.35881490.3062367X-RAY DIFFRACTION100
2.14-2.230.3011520.27592392X-RAY DIFFRACTION100
2.23-2.350.27471510.24592394X-RAY DIFFRACTION100
2.35-2.50.31391500.24422389X-RAY DIFFRACTION100
2.5-2.690.2811530.24232422X-RAY DIFFRACTION100
2.69-2.960.32481520.23232416X-RAY DIFFRACTION100
2.96-3.390.25091540.21772435X-RAY DIFFRACTION100
3.39-4.270.22711550.17212468X-RAY DIFFRACTION100
4.27-49.710.20981640.16062592X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.4247 Å / Origin y: -4.6604 Å / Origin z: 13.6115 Å
111213212223313233
T0.223 Å2-0.0244 Å20.019 Å2-0.1927 Å2-0.0197 Å2--0.2109 Å2
L2.0395 °2-0.3253 °2-0.1272 °2-1.1143 °2-0.1096 °2--2.1647 °2
S0.0089 Å °0.0352 Å °-0.0881 Å °0.0056 Å °-0.1379 Å °0.1567 Å °0.185 Å °-0.1183 Å °0.116 Å °
Refinement TLS groupSelection details: all

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