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- PDB-6pfx: D-alanyl transferase DltD from Enterococcus faecium -

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Basic information

Entry
Database: PDB / ID: 6pfx
TitleD-alanyl transferase DltD from Enterococcus faecium
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 / membrane => GO:0016020 / plasma membrane / Protein DltD / Protein DltD
Function and homology information
Biological speciesEnterococcus faecium TX0133A04 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 faecium
Authors: Shakhashiro, M. / Williamson, Z.A. / Korotkova, N. / Korotkov, K.V.
History
DepositionJun 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 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

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Assembly

Deposited unit
A: D-alanyl transferase DltD
B: D-alanyl transferase DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9654
Polymers92,7812
Non-polymers1842
Water11,349630
1
A: D-alanyl transferase DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4832
Polymers46,3911
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-alanyl transferase DltD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4832
Polymers46,3911
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.255, 76.434, 78.400
Angle α, β, γ (deg.)90.000, 117.725, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein D-alanyl transferase DltD


Mass: 46390.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium TX0133A04 (bacteria)
Gene: dltD, AWT83_05715, B4W81_00525, BU187_05285, BU190_00460, BU192_07235, BXT96_01745, CQR37_04475, CUM68_11350, CUS36_06310, DKP91_06765, DTPHA_600407, EB12_02182, NCTC13923_01752
Plasmid: pRSF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: A0A132P6N8, UniProt: Q3XZT4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.81 % / Description: prizm
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 0.1M sodium citrate pH 3.8, 25% PEG3350, 4% polypropylene glycol P400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 17, 2019
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33.04 Å / Num. obs: 121042 / % possible obs: 98 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.01 Å2 / Rpim(I) all: 0.076 / Rsym value: 0.117 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5330.74959480.6550.4920.90.53997.3
1.53-1.553.20.7460410.660.4740.8830.55898.4
1.55-1.583.40.68661110.6850.4290.8130.57298.8
1.58-1.623.50.62160720.7380.3820.7330.6299.1
1.62-1.653.50.54360680.8010.3320.6390.66398.9
1.65-1.693.50.561540.8010.310.5910.67599.1
1.69-1.733.40.42460670.8440.2660.5030.72599
1.73-1.783.30.34460500.8660.2240.4130.88298.4
1.78-1.833.10.30359980.8880.2050.3681.04797.5
1.83-1.893.50.27260840.9260.170.3221.15298.8
1.89-1.963.70.23360870.9450.1420.2741.34598.5
1.96-2.043.70.19360060.960.1190.2271.67598
2.04-2.133.50.16260840.970.1020.1921.9298.3
2.13-2.243.40.14460600.9740.0920.1722.16797.8
2.24-2.383.20.12460230.9790.0830.152.54797.5
2.38-2.562.80.10459230.980.0750.132.68796.1
2.56-2.823.20.09460260.9860.0620.1132.81597.3
2.82-3.233.30.08260470.9880.0530.0983.3297.2
3.23-4.073.20.06560670.9920.0430.0783.62897.5
4.07-33.043.20.05761260.9930.0380.0693.35796.6

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
HKL-2000716.1data scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O93

6o93


Resolution: 1.5→33.04 Å / SU ML: 0.1707 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6987
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 6394 5.29 %RANDOM SELECTION
Rwork0.1882 ---
obs0.1895 120980 97.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.21 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6347 0 12 630 6989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00666518
X-RAY DIFFRACTIONf_angle_d0.90068794
X-RAY DIFFRACTIONf_chiral_restr0.0684914
X-RAY DIFFRACTIONf_plane_restr0.00571137
X-RAY DIFFRACTIONf_dihedral_angle_d15.63462463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.29961430.27442900X-RAY DIFFRACTION74.06
1.52-1.530.31062320.27333813X-RAY DIFFRACTION98.04
1.53-1.550.29421960.25473851X-RAY DIFFRACTION98.35
1.55-1.570.27852050.24963878X-RAY DIFFRACTION98.77
1.57-1.590.27352110.24143921X-RAY DIFFRACTION98.92
1.59-1.610.26791990.21623904X-RAY DIFFRACTION99.11
1.61-1.640.2492160.20523859X-RAY DIFFRACTION98.93
1.64-1.660.22182180.20153839X-RAY DIFFRACTION98.85
1.66-1.690.23131950.20813919X-RAY DIFFRACTION99.08
1.69-1.720.23491840.2093903X-RAY DIFFRACTION98.93
1.72-1.740.22951910.20643900X-RAY DIFFRACTION98.84
1.74-1.780.22962040.20263879X-RAY DIFFRACTION98.41
1.78-1.810.24651990.19983825X-RAY DIFFRACTION97.96
1.81-1.850.21352090.193819X-RAY DIFFRACTION97.7
1.85-1.890.22992100.18483896X-RAY DIFFRACTION98.82
1.89-1.930.20642000.18123856X-RAY DIFFRACTION98.07
1.93-1.980.19912080.17983851X-RAY DIFFRACTION98.62
1.98-2.030.20952120.18223842X-RAY DIFFRACTION97.8
2.03-2.090.20652090.17873858X-RAY DIFFRACTION98.19
2.09-2.160.22911770.18063888X-RAY DIFFRACTION98.09
2.16-2.240.2242210.18383863X-RAY DIFFRACTION97.87
2.24-2.330.1962420.17213823X-RAY DIFFRACTION97.58
2.33-2.430.21852080.17333777X-RAY DIFFRACTION96.82
2.43-2.560.20852600.17713743X-RAY DIFFRACTION96.06
2.56-2.720.21742450.18383787X-RAY DIFFRACTION96.88
2.72-2.930.19752010.19023855X-RAY DIFFRACTION97.66
2.93-3.230.21142660.18823808X-RAY DIFFRACTION97.23
3.23-3.690.18472340.17523804X-RAY DIFFRACTION97.21
3.69-4.650.1741960.16363896X-RAY DIFFRACTION97.08
4.65-33.050.19893030.20173829X-RAY DIFFRACTION97.02

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