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- PDB-4de9: LytR-CPS2A-psr family protein YwtF (TagT) with bound octaprenyl p... -

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Basic information

Entry
Database: PDB / ID: 4de9
TitleLytR-CPS2A-psr family protein YwtF (TagT) with bound octaprenyl pyrophosphate lipid
ComponentsPutative transcriptional regulator ywtF
KeywordsMEMBRANE PROTEIN / Possible role in wall techoic acid synthesis
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / cell wall organization / transferase activity / plasma membrane
Similarity search - Function
Nucleotidyltransferase; domain 5 - #590 / LCP protein / : / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-VTP / Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.787 Å
AuthorsEberhardt, A. / Hoyland, C.N. / Vollmer, D. / Bisle, S. / Cleverley, R.M. / Johnsborg, O. / Havarstein, S. / Lewis, R.J. / Vollmer, W.
CitationJournal: Microb Drug Resist / Year: 2012
Title: Attachment of Capsular Polysaccharide to the Cell Wall in Streptococcus pneumoniae.
Authors: Eberhardt, A. / Hoyland, C.N. / Vollmer, D. / Bisle, S. / Cleverley, R.M. / Johnsborg, O. / Havarstein, L.S. / Lewis, R.J. / Vollmer, W.
History
DepositionJan 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator ywtF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7862
Polymers32,0631
Non-polymers7231
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.740, 65.740, 137.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

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Components

#1: Protein Putative transcriptional regulator ywtF


Mass: 32063.398 Da / Num. of mol.: 1 / Fragment: UNP residues 98-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ywtF, BSU35840 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q7WY78
#2: Chemical ChemComp-VTP / (2Z,6Z,10Z,14Z,18Z,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl trihydrogen diphosphate


Mass: 722.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68O7P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES 20% PEG 3350 0.2M MgCl2 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.787→47.5 Å / Num. all: 29369 / Num. obs: 29369 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.787→1.88 Å / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.787→32.87 Å / SU ML: 0.22 / σ(F): 0.13 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1486 5.08 %Random
Rwork0.1951 ---
all0.1964 29245 --
obs0.1964 29245 99.52 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.843 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.787→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 49 211 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051961
X-RAY DIFFRACTIONf_angle_d0.9042634
X-RAY DIFFRACTIONf_dihedral_angle_d14.891748
X-RAY DIFFRACTIONf_chiral_restr0.048300
X-RAY DIFFRACTIONf_plane_restr0.003334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7871-1.84470.33751200.29022486X-RAY DIFFRACTION100
1.8447-1.91070.31991230.25342491X-RAY DIFFRACTION100
1.9107-1.98720.25061220.2172487X-RAY DIFFRACTION100
1.9872-2.07760.24221370.20112481X-RAY DIFFRACTION100
2.0776-2.18710.22591430.19662510X-RAY DIFFRACTION100
2.1871-2.32410.2431350.19122467X-RAY DIFFRACTION100
2.3241-2.50350.23381460.18162506X-RAY DIFFRACTION100
2.5035-2.75530.23221360.19882525X-RAY DIFFRACTION100
2.7553-3.15370.23771380.19652547X-RAY DIFFRACTION100
3.1537-3.97230.20531530.18172574X-RAY DIFFRACTION100
3.9723-32.87550.18051330.19042685X-RAY DIFFRACTION97
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)
15.6710.85632.18456.40292.97036.75510.0905-0.2724-0.17230.1862-0.00360.709-0.0784-0.590.06270.12760.00210.04140.18430.10090.2228-25.9088.4614-9.3227
23.6874-0.85690.98962.20290.12942.1618-0.0707-0.0390.01870.09920.05140.263-0.0987-0.09460.00850.13990.0127-0.00240.16470.04960.1541-16.857315.7953-8.734
34.2041-1.20553.01890.6807-0.81393.873-0.1579-0.33730.16180.10140.12620.1122-0.1696-0.20610.0450.15330.01480.00540.13720.0210.1811-6.37066.81455.8644
43.36210.81220.96954.6622-1.08581.54030.1034-0.3431-0.21460.1645-0.0406-0.07840.0015-0.1624-0.04160.10470.00610.01460.22170.0150.0587-13.33669.9521-7.038
52.07612.0690.51582.1141.16538.4006-0.31020.7472-0.4864-0.75390.4388-0.41140.31110.2131-0.02090.22890.01070.0010.3322-0.00640.3137-12.27210.7372-20.7386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 51:95)
2X-RAY DIFFRACTION2chain 'A' and (resseq 96:152)
3X-RAY DIFFRACTION3chain 'A' and (resseq 153:243)
4X-RAY DIFFRACTION4chain 'A' and (resseq 244:305)
5X-RAY DIFFRACTION5chain 'A' and (resseq 306:322)

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