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- PDB-8i32: D-alanyl carrier protein mutant-S36A -

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Basic information

Entry
Database: PDB / ID: 8i32
TitleD-alanyl carrier protein mutant-S36A
ComponentsD-alanyl carrier protein
KeywordsLIGASE / Carrier protein / Lipoteichoic acid
Function / homology
Function and homology information


D-alanyl carrier activity / lipoteichoic acid biosynthetic process / cell wall organization / cytoplasm
Similarity search - Function
D-alanyl carrier protein / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
D-alanyl carrier protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJeon, H. / Lee, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of D-alanyl carrier protein at 2.09 Angstroms resolution.
Authors: Jeon, H.
History
DepositionJan 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-alanyl carrier protein
B: D-alanyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1983
Polymers18,1062
Non-polymers921
Water1,51384
1
A: D-alanyl carrier protein
hetero molecules

B: D-alanyl carrier protein


Theoretical massNumber of molelcules
Total (without water)18,1983
Polymers18,1062
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1530 Å2
ΔGint-18 kcal/mol
Surface area8370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.735, 157.955, 27.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D-alanyl carrier protein / DCP / D-alanine--poly(phosphoribitol) ligase subunit 2


Mass: 9053.144 Da / Num. of mol.: 2 / Mutation: S36A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: dltC, SAV0934 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A018
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG 8000 20.5% PEG 400 20% 100mM MgCl2 100mM pH 7.0 Tris-HCl

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.09→32.08 Å / Num. obs: 9164 / % possible obs: 99.8 % / Redundancy: 12.1 % / Rrim(I) all: 0.217 / Net I/σ(I): 18
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 885 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bpf

4bpf


Resolution: 2.1→32.054 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 473 5.28 %
Rwork0.2168 8484 -
obs0.2184 8957 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.22 Å2 / Biso mean: 34.7979 Å2 / Biso min: 17.74 Å2
Refinement stepCycle: final / Resolution: 2.1→32.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 6 84 1352
Biso mean--43.27 38.62 -
Num. residues----155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031281
X-RAY DIFFRACTIONf_angle_d0.4441733
X-RAY DIFFRACTIONf_chiral_restr0.041203
X-RAY DIFFRACTIONf_plane_restr0.003231
X-RAY DIFFRACTIONf_dihedral_angle_d2.443790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.1-2.180.343890.25828020100
2.18-2.260.3515870.2429779100
2.26-2.370.2962900.2437805100
2.37-2.490.2957860.2501786100
2.49-2.650.3543880.2405787100
2.65-2.850.3486900.247381299
2.85-3.140.319880.226279199
3.14-3.590.2943900.203480797
3.59-4.520.207890.171780297

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