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- PDB-7dxm: Crystal structure of DltD -

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Basic information

Entry
Database: PDB / ID: 7dxm
TitleCrystal structure of DltD
ComponentsProtein DltD
KeywordsTRANSFERASE / O-acyltransferase / dlt operon
Function / homologyDltD / D-alanyl-lipoteichoic acid biosynthesis DltD, Firmicutes / DltD protein / lipoteichoic acid biosynthetic process / plasma membrane / Protein DltD
Function and homology information
Biological speciesStreptococcus thermophilus LMG 18311 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsYan, X.X. / Zeng, Q. / Tian, L.F.
CitationJournal: Prog.Biochem.Biophys. / Year: 2022
Title: Crystal Structure of an O-acyltransfer Terminal Protein stDltD and Its Implications for dlt Operon-mediated D-alanylation of S. thermophilus.
Authors: Zeng, Q. / Tian, L.F. / Liu, Y.P. / Yan, X.X. / Xu, W.Q.
History
DepositionJan 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein DltD
B: Protein DltD
C: Protein DltD
D: Protein DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,7008
Polymers183,3164
Non-polymers3844
Water70339
1
A: Protein DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0213
Polymers45,8291
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9252
Polymers45,8291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein DltD


Theoretical massNumber of molelcules
Total (without water)45,8291
Polymers45,8291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9252
Polymers45,8291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.273, 109.92, 282.377
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein DltD


Mass: 45829.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus LMG 18311 (bacteria)
Strain: LMG 18311 / Gene: dltD / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5M4V2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.63 Å3/Da / Density meas: 53.22 Mg/m3 / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% glycerol, 14% [w/v] PEG6000, 170 mM (NH4)2SO4)

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.96→40 Å / Num. obs: 38815 / % possible obs: 99.2 % / Redundancy: 4 % / CC1/2: 0.984 / Rpim(I) all: 0.105 / Rrim(I) all: 0.215 / Net I/σ(I): 10.85
Reflection shellResolution: 2.96→3.01 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1904 / CC1/2: 0.554 / Rpim(I) all: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMA

3bma


Resolution: 2.96→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.228 1884 -
Rwork0.216 --
obs-36928 98.1 %
Refinement stepCycle: LAST / Resolution: 2.96→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12726 0 20 39 12785

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