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- PDB-6o93: D-alanyl transferase DltD from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 6o93
TitleD-alanyl transferase DltD from Enterococcus faecalis
ComponentsD-alanyl transferase DltD
KeywordsTRANSFERASE / D-alanine / D-alanylation / lipoteichoic acid / LTA / D-alanyl lipoteichoic acid / cell wall / Gram-positive bacteria
Function / homologyDltD / D-alanyl-lipoteichoic acid biosynthesis DltD, Firmicutes / DltD protein / lipoteichoic acid biosynthetic process / plasma membrane / PHOSPHATE ION / Protein DltD
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.178 Å
AuthorsShakhashiro, M. / Korotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: To Be Published
Title: D-alanyl transferase DltD from Enterococcus faecalis
Authors: Shakhashiro, M. / Williamson, Z.A. / Korotkova, N. / Korotkov, K.V.
History
DepositionMar 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanyl transferase DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,52112
Polymers45,7351
Non-polymers78611
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.750, 102.750, 205.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-504-

PO4

21A-640-

HOH

31A-744-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein D-alanyl transferase DltD


Mass: 45735.000 Da / Num. of mol.: 1 / Fragment: residues 31-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria)
Strain: ATCC 700802 / V583 / Gene: dltD, EF_2746 / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q830N3

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.43 Å3/Da / Density % sol: 64.12 % / Description: hexagonal prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M Na2HPO4-citric acid pH 4.2, 1.6 M Na2HPO4, 0.4 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 2, 2019
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror water
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.178→45.962 Å / Num. obs: 31722 / % possible obs: 92.2 % / Redundancy: 6.934 % / Biso Wilson estimate: 28.912 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.194 / Χ2: 0.95 / Net I/σ(I): 10.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.18-2.234.8510.8351.7521940.6360.92887.6
2.23-2.36.910.6942.7422760.8410.74894.9
2.3-2.366.8560.5833.2122320.8740.62994.6
2.36-2.446.890.5513.4721740.8840.59394.4
2.44-2.516.8720.4783.9821030.9180.51594.2
2.51-2.66.8510.4284.520210.9260.46294
2.6-2.76.9770.3935.0319790.9390.42393.7
2.7-2.817.2320.3695.6118680.9460.39693.4
2.81-2.947.3160.2937.0518190.9680.31493
2.94-3.087.2720.2538.0517090.9780.27292.8
3.08-3.257.290.18611.0416340.9840.19992.4
3.25-3.447.2710.13514.6115670.9920.14592.1
3.44-3.687.2780.10717.9714580.9950.11591.6
3.68-3.987.2980.07922.6913480.9970.08591.1
3.98-4.367.2780.07124.912540.9980.07690.7
4.36-4.877.3050.06427.0111350.9980.06890.1
4.87-5.627.2590.07323.7810010.9970.07989.1
5.62-6.897.2010.07921.938620.9960.08588.4
6.89-9.747.0040.04630.766830.9990.04987.1
9.74-45.9626.2070.031404050.9990.03484.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.95 Å45.96 Å
Translation4.95 Å45.96 Å

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018 BUILT=20180808data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180808data scaling
PHASER2.8.2phasing
PHENIXdev_3139refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BMA

3bma


Resolution: 2.178→45.962 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 19.6 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1660 5.23 %RANDOM SELECTION
Rwork0.1831 ---
obs0.1849 31721 92.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.49 Å2 / Biso mean: 31.07 Å2 / Biso min: 11.68 Å2
Refinement stepCycle: final / Resolution: 2.178→45.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 0 66 263 3526
Biso mean--59.81 30.89 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0020.0183303
X-RAY DIFFRACTIONf_angle_d0.453.8834462
X-RAY DIFFRACTIONf_dihedral_angle_d12.408179.9821980
X-RAY DIFFRACTIONf_chiral_restr0.0370.139469
X-RAY DIFFRACTIONf_plane_restr0.0030.032577
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.178-2.21210.3091440.2952137228179
2.2121-2.24830.30041500.2512615276595
2.2483-2.28710.27111440.24052624276895
2.2871-2.32870.26961330.22352583271695
2.3287-2.37350.25671360.22242616275295
2.3735-2.42190.22621430.22442594273794
2.4219-2.47460.23131420.21612585272795
2.4746-2.53210.21961220.19832598272095
2.5321-2.59550.22151420.20442587272994
2.5955-2.66560.26751420.19322603274594
2.6656-2.74410.25131560.20332530268694
2.7441-2.83260.2241490.19842563271294
2.8326-2.93380.25091320.20462582271494
2.9338-3.05130.25031630.19392507267093
3.0513-3.19010.21921380.18242564270293
3.1901-3.35830.22191320.17712561269393
3.3583-3.56860.23131580.17222497265592
3.5686-3.8440.18041600.14772492265292
3.844-4.23060.13921320.13282516264892
4.2306-4.84220.1881080.12882530263891
4.8422-6.09840.20151170.15522505262290
6.0984-45.97260.17331400.18392436257689
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5768-0.3106-1.55980.73740.34892.31490.1447-0.2620.41770.1377-0.02580.061-0.1007-0.0459-0.08980.2278-0.02790.02460.1598-0.00680.1536-22.1598-21.869815.8243
21.13530.5593-0.20612.01050.04060.49590.0379-0.02550.07460.0234-0.0367-0.0124-0.0046-0.00180.00450.1696-0.00960.0070.16060.01270.1036-14.3859-32.57739.1626
32.41051.28340.10382.08390.44050.69220.0561-0.03240.14690.0874-0.08680.20570.0058-0.10350.02570.20390.021-0.00750.1210.06570.1043-23.7042-32.081312.2751
40.6907-1.23860.04496.3537-1.63912.69310.0007-0.41030.16640.9199-0.1322-0.66370.02910.30310.11290.3798-0.0703-0.15030.4339-0.00730.37717.0404-28.075527.4809
52.7555-1.15510.79892.6442-0.32582.0031-0.0237-0.0866-0.00940.1139-0.0091-0.20240.04740.12850.0210.1655-0.01810.060.16440.03680.15310.3913-36.08618.276
61.07550.0501-0.36482.0430.33031.37750.0618-0.05340.1250.0139-0.0626-0.4088-0.03950.1711-0.00850.1397-0.03390.02330.17940.02690.23833.0826-26.23938.3443
72.5813-1.0072-0.62051.080.27611.75330.02010.22790.0343-0.1095-0.0976-0.0836-0.141-0.15140.06170.28880.02310.04240.24030.0430.1523-2.1855-35.8577-5.9756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 70 )A27 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 183 )A71 - 183
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 245 )A184 - 245
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 284 )A246 - 284
5X-RAY DIFFRACTION5chain 'A' and (resid 285 through 334 )A285 - 334
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 393 )A335 - 393
7X-RAY DIFFRACTION7chain 'A' and (resid 394 through 424 )A394 - 424

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