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- PDB-8i31: D-alanyl carrier protein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8i31
TitleD-alanyl carrier protein
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: 2.28 Å
AuthorsJeon, H. / Lee, I.-G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of D-alanyl carrier protein at 2.3 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
C: D-alanyl carrier protein
D: D-alanyl carrier protein


Theoretical massNumber of molelcules
Total (without water)36,2774
Polymers36,2774
Non-polymers00
Water724
1
A: D-alanyl carrier protein

B: D-alanyl carrier protein


Theoretical massNumber of molelcules
Total (without water)18,1382
Polymers18,1382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1380 Å2
ΔGint-17 kcal/mol
Surface area8340 Å2
MethodPISA
2
C: D-alanyl carrier protein

D: D-alanyl carrier protein


Theoretical massNumber of molelcules
Total (without water)18,1382
Polymers18,1382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1370 Å2
ΔGint-17 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.137, 63.968, 77.145
Angle α, β, γ (deg.)90.00, 93.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 9069.144 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, Magnesium chloride, pH 7.5 HEPES, Sodium Thiocyanate

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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: 0.97927 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 14764 / % possible obs: 99.74 % / Redundancy: 7.2 % / CC1/2: 0.996 / Net I/σ(I): 12.6
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 1456 / CC1/2: 0.944 / CC star: 0.986

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bph

4bph


Resolution: 2.28→32.97 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2385 714 4.86 %
Rwork0.2187 --
obs0.2197 14680 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 0 4 2548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072592
X-RAY DIFFRACTIONf_angle_d0.9283500
X-RAY DIFFRACTIONf_dihedral_angle_d7.144328
X-RAY DIFFRACTIONf_chiral_restr0.049408
X-RAY DIFFRACTIONf_plane_restr0.007464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.460.30621370.24152737X-RAY DIFFRACTION98
2.46-2.710.28211530.25372779X-RAY DIFFRACTION100
2.71-3.10.31871320.26212800X-RAY DIFFRACTION100
3.1-3.90.22291300.21742824X-RAY DIFFRACTION100
3.9-32.970.19651620.18512826X-RAY DIFFRACTION99

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