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- PDB-3e7w: Crystal structure of DLTA: Implications for the reaction mechanis... -

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Basic information

Entry
Database: PDB / ID: 3e7w
TitleCrystal structure of DLTA: Implications for the reaction mechanism of non-ribosomal peptide synthetase (NRPS) adenylation domains
ComponentsD-alanine--poly(phosphoribitol) ligase subunit 1
KeywordsLIGASE / DLTA / NON-RIBOSOMAL PEPTIDE SYNTHETASE / NRPS / ADENYLATION DOMAIN / D-alanylation / D-alanine-Dalanyl / AMP / Cytoplasm
Function / homology
Function and homology information


D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
D-alanine--D-alanyl carrier protein ligase / D-alanine:D-alanyl carrier protein ligase-like / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...D-alanine--D-alanyl carrier protein ligase / D-alanine:D-alanyl carrier protein ligase-like / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / D-alanine--D-alanyl carrier protein ligase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsYonus, H. / Neumann, P. / Zimmermann, S. / May, J.J. / Marahiel, M.A. / Stubbs, M.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains
Authors: Yonus, H. / Neumann, P. / Zimmermann, S. / May, J.J. / Marahiel, M.A. / Stubbs, M.T.
History
DepositionAug 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanine--poly(phosphoribitol) ligase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3803
Polymers56,9371
Non-polymers4422
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.564, 94.990, 132.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein D-alanine--poly(phosphoribitol) ligase subunit 1 / DLTA PROTEIN / D-alanine-activating enzyme / DAE / D-alanine-D-alanyl carrier protein ligase / DCL


Mass: 56937.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dltA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P39581, EC: 6.1.1.13
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M sodium citrate, 0.2M ammonium acetate, 20% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9123 Å / Relative weight: 1
ReflectionNumber: 64552 / Rmerge(I) obs: 0.07 / Χ2: 1.21 / D res high: 3.04 Å / D res low: 99 Å / Num. obs: 20798 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obsChi squared
8.889984.810.0431.73
7.058.889710.0471.479
6.167.05239710.0541.391
5.596.1625198.210.0591.404
5.195.59110298.110.0541.32
4.895.19103298.710.051.286
4.644.89234999.310.051.328
4.444.64655798.910.051.203
4.274.44121999.610.0551.323
4.124.27702099.210.0621.276
3.994.12252499.210.061.292
3.883.99336298.810.0641.082
3.783.8899.410.0751.176
3.683.7899.210.081.239
3.63.6899.810.0831.101
3.523.699.610.0991.16
3.453.5299.910.1061.122
3.393.4599.510.1181.145
3.333.3999.610.1211.073
3.273.3399.510.1461.053
3.223.2799.510.1611.037
3.173.2299.410.1761.029
3.123.1799.510.2021.019
3.083.1299.310.2310.985
3.043.0889.910.2571.03
ReflectionResolution: 2.28→30 Å / Num. all: 26455 / Num. obs: 25439 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.89 % / Biso Wilson estimate: 38.783 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.075 / Net I/σ(I): 13.92
Reflection shellResolution: 2.28→2.4 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 9194 / Num. unique all: 3720 / Num. unique obs: 3362 / Rsym value: 0.35 / % possible all: 90.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
CNS1.1refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→19.92 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.816 / Data cutoff high absF: 4358166 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1503 5.9 %RANDOM
Rwork0.205 ---
all-26455 --
obs-25261 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.715 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso max: 95.52 Å2 / Biso mean: 41.12 Å2 / Biso min: 16.74 Å2
Baniso -1Baniso -2Baniso -3
1-22.36 Å20 Å20 Å2
2---7.42 Å20 Å2
3----14.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.28→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 28 367 4450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.28→2.31 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.322 36 7.3 %
Rwork0.306 460 -
all-496 -
obs-496 58.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramamp.top
X-RAY DIFFRACTION3amp.paramion.top
X-RAY DIFFRACTION4ion.param

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