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- PDB-4bpg: Crystal structure of Bacillus subtilis DltC -

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Basic information

Entry
Database: PDB / ID: 4bpg
TitleCrystal 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
D-alanyl carrier protein
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYonus, H. / Zimmermann, 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 / Other
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Aug 26, 2015Group: Database references
Revision 1.4Dec 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
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_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
B: D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)20,3342
Polymers20,3342
Non-polymers00
Water79344
1
A: D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 2
B: D-ALANINE--POLY(PHOSPHORIBITOL) LIGASE SUBUNIT 2

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


Theoretical massNumber of molelcules
Total (without water)40,6694
Polymers40,6694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area4350 Å2
ΔGint-26.3 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.680, 72.680, 110.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 10167.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHOSERINE FROM S36 MODIFICATION WITH COFACTOR / 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 / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 5.7
Details: 0.1 M SODIUM ACETATE, 0.2 M AMMONIUM ACETATE, 30 % PEG 4000, PH 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→62.94 Å / Num. obs: 9306 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 38.76 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

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

4bpf


Resolution: 2.2→23.909 Å / SU ML: 0.31 / σ(F): 1.52 / Phase error: 23.17 / Stereochemistry target values: ML / Details: RESIDUES 81-86 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2369 791 4.8 %
Rwork0.2091 --
obs0.2105 9293 99.96 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.93 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 51.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.3541 Å20 Å20 Å2
2---1.3541 Å20 Å2
3---1.8477 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 0 44 1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021320
X-RAY DIFFRACTIONf_angle_d0.5341796
X-RAY DIFFRACTIONf_dihedral_angle_d15.048499
X-RAY DIFFRACTIONf_chiral_restr0.04211
X-RAY DIFFRACTIONf_plane_restr0.002237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.24780.381760.2739939X-RAY DIFFRACTION100
2.2478-2.30010.3164570.2657977X-RAY DIFFRACTION100
2.3001-2.35750.2964500.2723988X-RAY DIFFRACTION100
2.3575-2.42120.2835480.24111002X-RAY DIFFRACTION100
2.4212-2.49240.2523520.2271969X-RAY DIFFRACTION100
2.4924-2.57270.2666570.23969X-RAY DIFFRACTION100
2.5727-2.66460.2646450.2217983X-RAY DIFFRACTION100
2.6646-2.77110.2301400.2119996X-RAY DIFFRACTION100
2.7711-2.8970.2747440.19881001X-RAY DIFFRACTION100
2.897-3.04950.206390.1995997X-RAY DIFFRACTION100
3.0495-3.24010.2429550.1978951X-RAY DIFFRACTION100
3.2401-3.48960.2514400.20181014X-RAY DIFFRACTION100
3.4896-3.83940.1937500.1762981X-RAY DIFFRACTION100
3.8394-4.3920.2637410.1773993X-RAY DIFFRACTION100
4.392-5.52220.1815490.197995X-RAY DIFFRACTION100
5.5222-23.91070.2031480.2036981X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9258-2.0579-0.96889.38120.77653.30070.00810.32270.10020.0416-0.1658-0.2672-0.07470.02020.13030.25580.0109-0.07630.2494-0.01730.0983-20.710914.38183.3359
29.30511.76272.4351.72460.31085.84060.694-0.0321-0.31580.5817-0.1292-0.18120.8799-0.0205-0.47420.55650.0561-0.19840.2161-0.05790.2151-14.450819.741124.5072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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