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

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Basic information

Entry
Database: PDB / ID: 4bph
TitleHigh resolution crystal structure of Bacillus subtilis DltC
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
4'-PHOSPHOPANTETHEINE / D-alanyl carrier protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.4Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4944
Polymers10,0871
Non-polymers4073
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.207, 49.207, 146.264
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-255-

PNS

21A-2010-

HOH

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Components

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


Mass: 10087.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SERINE 36 MODIFIED WITH COFACTOR PHOSPHOPANTETHEINE
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: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSERINE 36 MODIFIED WITH PHOSPHOPANTETHEINE

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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: 2.45 Å3/Da / Density % sol: 49.82 % / Description: NONE
Crystal growpH: 5.6
Details: 95 MM SODIUM-CITRATE, 19% PEG 4000, 19% 2-PROPANOL, 8% GLYCEROL, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 8, 2008
RadiationMonochromator: COPPER ANODE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40.93 Å / Num. obs: 10436 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 19.5 % / Biso Wilson estimate: 28.52 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 19.8 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BPF

4bpf


Resolution: 1.8→42.614 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 500 4.8 %
Rwork0.1673 --
obs0.1696 10431 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 24 56 769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004733
X-RAY DIFFRACTIONf_angle_d0.811999
X-RAY DIFFRACTIONf_dihedral_angle_d13.804276
X-RAY DIFFRACTIONf_chiral_restr0.042113
X-RAY DIFFRACTIONf_plane_restr0.003131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.98120.22511080.17462419X-RAY DIFFRACTION100
1.9812-2.26790.21671300.14722401X-RAY DIFFRACTION100
2.2679-2.85720.23731300.16882463X-RAY DIFFRACTION100
2.8572-42.62640.20791320.17072648X-RAY DIFFRACTION100

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