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- PDB-4bpf: High resolution crystal structure of Bacillus subtilis DltC S36A -

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Basic information

Entry
Database: PDB / ID: 4bpf
TitleHigh resolution crystal structure of Bacillus subtilis DltC S36A
ComponentsD-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 2
KeywordsLIGASE / LIPOTEICHOIC ACID / D-ALANYLATION / PEPTIDYL-CARRIER-PROTEIN / ACYL-CARRIER-PROTEIN
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 / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
D-alanyl carrier protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.01 Å
AuthorsZimmermann, S. / Neumann, P. / Stubbs, M.T.
CitationJournal: FEBS Lett. / Year: 2015
Title: High-Resolution Structures of the D-Alanyl Carrier Protein (Dcp) Dltc from Bacillus Subtilis Reveal Equivalent Conformations of Apo- and Holo-Forms
Authors: Zimmermann, S. / Pfennig, S. / Neumann, P. / Yonus, H. / Weininger, U. / Kovermann, M. / Balbach, J. / Stubbs, M.T.
History
DepositionMay 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 26, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)10,1181
Polymers10,1181
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.590, 37.222, 37.676
Angle α, β, γ (deg.)90.00, 114.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 2 / D-ALANYL CARRIER PROTEIN / DCP / DLTC


Mass: 10118.137 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39579, EC: 6.1.1.13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLAST 8 RESIDUES FROM EXPRESSION CONSTRUCT

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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: 43.84 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% W/V PEG 3350, 100 MM BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.04→100 Å / Num. obs: 45688 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 8.42 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.9
Reflection shellResolution: 1.04→1.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.01→17.278 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 15.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.156 1380 3.1 %
Rwork0.1293 --
obs0.1302 44007 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.01→17.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 0 0 137 846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01863
X-RAY DIFFRACTIONf_angle_d1.3531193
X-RAY DIFFRACTIONf_dihedral_angle_d14.388340
X-RAY DIFFRACTIONf_chiral_restr0.118131
X-RAY DIFFRACTIONf_plane_restr0.007161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.04610.27661290.24864175X-RAY DIFFRACTION94
1.0461-1.0880.21541370.1944126X-RAY DIFFRACTION95
1.088-1.13750.17061300.16364231X-RAY DIFFRACTION96
1.1375-1.19740.17691160.13824249X-RAY DIFFRACTION96
1.1974-1.27240.13761370.12424266X-RAY DIFFRACTION96
1.2724-1.37070.1551450.11554275X-RAY DIFFRACTION97
1.3707-1.50850.13581650.10624308X-RAY DIFFRACTION98
1.5085-1.72660.13251250.10364357X-RAY DIFFRACTION98
1.7266-2.17470.16041400.11814415X-RAY DIFFRACTION99
2.1747-17.2810.1511560.1314225X-RAY DIFFRACTION94

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