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- PDB-7dd0: Crystal structure of the N-terminal domain of TagH from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 7dd0
TitleCrystal structure of the N-terminal domain of TagH from Bacillus subtilis
ComponentsTeichoic acids export ATP-binding protein TagH
KeywordsTRANSPROT PROTEIN / TRANSLOCASE / ABC transporter / ATP-binding protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type teichoic-acid transporter / ABC-type teichoic acid transporter activity / ATP binding / plasma membrane
Similarity search - Function
Teichoic acids export ATP-binding protein tagH. / ABC transporter, teichoic acids export TagH-like / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Teichoic acids export ATP-binding protein TagH
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKo, T.P. / Yang, C.S. / Wang, Y.C. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2311-B241-001 Taiwan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the N-terminal domain of TagH reveals a potential drug targeting site.
Authors: Yang, C.S. / Huang, W.C. / Ko, T.P. / Wang, Y.C. / Wang, A.H. / Chen, Y.
History
DepositionOct 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Teichoic acids export ATP-binding protein TagH
B: Teichoic acids export ATP-binding protein TagH
C: Teichoic acids export ATP-binding protein TagH
D: Teichoic acids export ATP-binding protein TagH


Theoretical massNumber of molelcules
Total (without water)128,7094
Polymers128,7094
Non-polymers00
Water5,783321
1
A: Teichoic acids export ATP-binding protein TagH
C: Teichoic acids export ATP-binding protein TagH


Theoretical massNumber of molelcules
Total (without water)64,3542
Polymers64,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-9 kcal/mol
Surface area22360 Å2
MethodPISA
2
B: Teichoic acids export ATP-binding protein TagH
D: Teichoic acids export ATP-binding protein TagH


Theoretical massNumber of molelcules
Total (without water)64,3542
Polymers64,3542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-15 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.735, 90.667, 91.213
Angle α, β, γ (deg.)90.000, 91.766, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEU(chain 'A' and (resid 2 through 16 or resid 35 through 257))AA2 - 162 - 16
12GLYGLYGLUGLU(chain 'A' and (resid 2 through 16 or resid 35 through 257))AA35 - 25735 - 257
23LYSLYSLEULEU(chain 'B' and (resid 2 through 16 or resid 35 through 257))BB2 - 162 - 16
24GLYGLYGLUGLU(chain 'B' and (resid 2 through 16 or resid 35 through 257))BB35 - 25735 - 257
35LYSLYSLEULEU(chain 'C' and resid 2 through 257)CC2 - 162 - 16
36GLYGLYGLUGLU(chain 'C' and resid 2 through 257)CC35 - 25735 - 257
47LYSLYSLEULEU(chain 'D' and (resid 2 through 16 or resid 35 through 257))DD2 - 162 - 16
48GLYGLYGLUGLU(chain 'D' and (resid 2 through 16 or resid 35 through 257))DD35 - 25735 - 257

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Components

#1: Protein
Teichoic acids export ATP-binding protein TagH / Teichoic acid-transporting ATPase


Mass: 32177.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: tagH, BSU35700
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P42954, ABC-type teichoic-acid transporter
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol (PEG) 3,000 and 0.1 M sodium citrate (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 24, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→19.735 Å / Num. obs: 32572 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 57.98 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.495 / Num. unique obs: 3161

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.73 Å / SU ML: 0.4172 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2349 1986 6.1 %
Rwork0.1856 30567 -
obs0.1886 32553 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 0 322 8315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00388138
X-RAY DIFFRACTIONf_angle_d0.771110904
X-RAY DIFFRACTIONf_chiral_restr0.04871178
X-RAY DIFFRACTIONf_plane_restr0.00441393
X-RAY DIFFRACTIONf_dihedral_angle_d21.28853084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.41651310.29732105X-RAY DIFFRACTION94.95
2.77-2.840.31081460.27262208X-RAY DIFFRACTION99.66
2.84-2.930.35271470.26992188X-RAY DIFFRACTION99.66
2.93-3.020.34381260.25882173X-RAY DIFFRACTION99.65
3.02-3.130.30211530.23532204X-RAY DIFFRACTION99.58
3.13-3.250.33191490.2312192X-RAY DIFFRACTION99.74
3.25-3.40.27621410.22182199X-RAY DIFFRACTION99.57
3.4-3.580.28751400.19912175X-RAY DIFFRACTION99.31
3.58-3.80.221440.17422195X-RAY DIFFRACTION99.41
3.8-4.090.20941420.16112208X-RAY DIFFRACTION99.32
4.09-4.50.18421430.14672201X-RAY DIFFRACTION99.49
4.5-5.140.15911430.14142193X-RAY DIFFRACTION98.94
5.14-6.440.21231450.17472228X-RAY DIFFRACTION99.33
6.44-19.730.2041360.16262098X-RAY DIFFRACTION92.47

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